Assays for Affinity Profiling of Nucleic Acid Binding Proteins

ABSTRACT

Methods, compositions and kits are disclosed for assays to determine the binding affinity of DNA-binding proteins or RNA-binding proteins for their corresponding recognition site(s). In particular, assays are disclosed for measuring binding affinities when either the binding protein, or the recognition sequence of the recognition site, or cofactor proteins, contain one or more mutations. The disclosed assays can thus be utilized to measure the effect on transcription factor binding caused by mutations within the recognition site, or mutations within the binding domain of the protein, and to provide binding affinity information that can be correlated with altered gene regulation and expression. The disclosed assays can be personalized to a specific person or organism, with the measured binding affinities based upon an individual&#39;s specific binding proteins and recognition sites. Furthermore, embodiments are capable of measuring binding affinities between multiple binding proteins and multiple recognition sites through an entirely in vitro process.

FIELD OF THE INVENTION

The presently disclosed methods and kits are related to assays formeasuring the binding affinity of DNA-binding proteins or RNA-bindingproteins for their corresponding recognition site(s). Specifically,assays are disclosed for measuring the binding affinity of a DNA-bindingor RNA-binding domain of a binding protein, such as a transcriptionfactor, for a recognition site within a nucleic acid. Depending upon theassay, the recognition sequence of the recognition site at issue maycontain one or more mutations, such as SNPs, that affect the bindingaffinity of the relevant binding protein(s). The disclosed assays arecapable of measuring binding affinities based upon a specific person ororganism's binding proteins and recognition sites, thus enablingcorrelation of mutations affecting binding affinities with theircorresponding changes, such as changes within gene expression andregulation that affect the diagnosis and/or treatment of variousdiseases and conditions.

BACKGROUND OF THE INVENTION

Nucleic acid binding proteins, namely DNA-binding proteins andRNA-binding proteins, are proteins that bind to either deoxyribonucleicacid (DNA) or ribonucleic acid (RNA). The binding can be non-specific,specific for a particular recognition site, or specific for a pluralityof recognition sites, with recognition sites consisting of a specificrecognition sequence of DNA or RNA. Examples of DNA-binding proteins aretranscription factors, polymerases, nucleases, and histones. Theseproteins perform such functions as regulating transcription, cleavingDNA, and packing DNA into nucleosomes. Variation in these functions,such as the regulation of transcription by transcription factors, isbelieved to be responsible for many genetic differences betweenindividuals that lead to phenotypic differences. (See, e.g., Kasowski etal., “Variation in Transcription Factor Binding Among Humans,” Science,328: 232-235 (2010); and Zheng et al., “Genetic analysis of variation intranscription factor binding in yeast,” Nature, 464: 1187-1191 (2010)).Examples of RNA-binding proteins are translation initiation factors thatbind with messenger RNA (mRNA), small nuclear ribonucleoproteins(snRNPs), and RNA editing proteins such as RNA specific adenosinedeaminase. These RNA binding proteins perform such functions asregulating translation and RNA splicing and editing. Additionally,studies have shown that mutations such as single-nucleotidepolymorphisms (SNPs), insertions, and deletions among either therecognition sequences or the genes which encode binding proteins cancause significant phenotypic changes. (See, e.g., Kasowski et al.,Science, 328: 232-235 (2010); Zheng et al., Nature, 464: 1187-1191(2010); and Grant et al., “Variant of transcription factor 7-like 2(TCF7L2) gene confers risk of type 2 diabetes,” Nature Genetics, 38(3):320-323 (2006)).

Previous assay methods to measure the binding affinity between a bindingprotein and its corresponding recognition site include chromatinimmunoprecipitation with subsequent analysis by microarrays orsequencing, protein binding microarrays, and related techniques usingsurface plasmon resonance that followed early techniques to studyingDNA-protein interactions such as DNA footprinting assays. (See, e.g.,Galas and Schmitz, “DNAase footprinting: a simple method for thedetection of protein-DNA binding specificity,” Nucleic Acids Research,5(9): 3157-3170 (1978)). Approaches using chromatin immunoprecipitationwith microarrays generally follow a protocol of fixing protein-nucleicacid complexes in vivo, such as with formaldehyde, lysing the cells,fragmenting the DNA, such as through sonication, immunoprecipitating thebinding proteins of interest, extracting and purifying the associatednucleic acid fragments, and detecting these fragments with the array.(See, e.g., Horak and Snyder, “ChIP-chip: A Genomic Approach forIdentifying Transcription Factor Binding Sites,” Methods in Enzymology,350: 469-483 (2002)). Disadvantages of this technique include therequirement of specific antibodies for each binding protein of interest,and in addition to the added complexity and cost of such a requirement,there are binding proteins for which an antibody may not be available,or for which the conditions and time points enabling the antibody'sexpression and activity are unknown. (See, e.g., Mukherjee et al.,“Rapid analysis of the DNA-binding specificities of transcriptionfactors with DNA microarrays,” Nature Genetics, 36(12): 1331-1339(2004)). Alternative chromatin immunoprecipitation techniques utilizesubsequent sequencing in place of microarrays to identify the sequencesthat are bound by the binding proteins. (See, e.g., Robertson et al.,“Genome-wide profiles of STAT1 DNA association using chromatinimmunoprecipitation and massively parallel sequencing,” Nature Methods,4(8): 651-657 (2007)). However, specific antibodies must still beprocured regardless of the change in the subsequent mode of analysis,and both techniques are also dependent upon the in vivo component offixing binding protein-nucleic acid complexes, thus complicating theprocess of analyzing particular binding proteins and/or recognitionsites of interest to a researcher or clinician.

Protein binding microarrays allow the entire assay to be performed invitro, and require the production of a double-stranded nucleic acidarray, such as a spotted double-stranded DNA array. (See, Mukherjee etal., Nature Genetics, 36(12): 1331-1339 (2004)). Binding proteins ofinterest are then introduced to the array with subsequent detection ofthe bound binding proteins. Such arrays, however, are limited to usingthe exact recognition sites within the double-stranded sequences spottedor otherwise produced upon the array. Mutations within recognitionsequences such as SNPs, insertions, deletions, inversions, or acombination thereof, can drastically affect the binding affinity that aparticular binding protein will have with that mutated recognition site.This can be especially important with regard to binding proteins whichbind to multiple sequences, as these binding proteins will not bespecific to only one recognition site, and additional changes to therecognition sequence of a possible recognition site through one or moremutations can substantially alter, among other process, regulationmechanisms employing competitive binding among multiple nucleic acidbinding proteins. (See, e.g., Wang, “Finding Primary Targets ofTranscriptional Regulators,” Cell Cycle, 4(3): 356-357 (2005); andBulyk, “Protein Binding Microarrays for the Characterization ofProtein-DNA Interactions,” Advances in Biochemical EngineeringBiotechnology, 104: 65-85 (2007)). Furthermore, while related assaysutilizing surface plasmon resonance can provide quantitative kineticdata, such assays are not easily scalable. (See, e.g., Bulyk, Advancesin Biochemical Engineering Biotechnology, 104: 65-85 (2007); andMukherjee et al., Nature Genetics, 36(12): 1331-1339 (2004)).

Additionally, some binding proteins operate in association with othermolecules within their overall binding mechanism in various conditions.For example, transcription elongation factors GreA and GreB bind withand induce nucleolytic activity in RNA polymerase. (See, Laptenko etal., “Transcript cleavage factors GreA and GreB act as transientcatalytic components of RNA polymerase,” The EMBO Journal, 22: 6322-6334(2003)). Many DNA-binding proteins function in concert with cofactors aswell, such as Mcml of the MADS box family of transcription factors,which bind with high specificity and affinity to their correspondingrecognition sites but that require interaction with different cofactorssuch as al or Stel2. (See, Mead et al., “Interactions of the Mcml MADSBox Protein with Cofactors That Regulate Mating in Yeast,” Molecular andCellular Biology, 22(13): 4607-4621 (2002)). Non-protein molecules mayalso affect the interaction of a binding protein with a recognitionsequence, such as miRNAs or siRNAs and their affect on the bindingaffinities of RNA-binding proteins. (See, Jacobsen et al., “Signaturesof RNA binding proteins globally coupled to effective microRNA targetsites,” Genome Research, 20: 1010-1019 (2010)). Thus, mutations thataffect the interaction between a binding protein and its accessorymolecules, such as cofactor proteins or miRNAs, can directly affectbinding affinities through, for instance, changes in certain residueswhich are crucial for proper interaction of a binding protein with itscofactors. (See, Mead et al., Molecular and Cellular Biology, 22(13):4607-4621 (2002)).

Therefore, these previous methods fail to meet the ongoing need topersonalize diagnostic and treatment options for individual patients instraightforward and cost-effective manner, and also fail to enableresearch of binding affinities of interest that accounts for possiblemutations within a recognition sequence, including mutations that arerare and/or previously unknown. In addition to the continuing need forimproved methods to measure the binding affinity of binding proteins forvarious recognition sites, there is also a need for improved methods tomeasure the differences effected in binding affinities when either thesequence of the gene encoding the binding protein, or the recognitionsequence of the recognition site, or both, possess one or moremutations. As discussed above, mutations which affect the bindingaffinity of a binding protein can cause significant phenotypic changes.For example, the presence of SNPs can alter binding affinitiessufficiently to cause corresponding differences in gene expression, thuseffecting a functional genetic variation. (See, e.g., Kasowski et al.,Science, 328: 232-235 (2010); Zheng et al., Nature, 464: 1187-1191(2010); and Grant et al., Nature Genetics, 38(3): 320-323 (2006)).Assays to detect and measure these binding affinity changes are usefulin diagnosing and treating conditions, such as SNPs within transcriptionfactor 7-like 2 (TCF7L2) being correlated with an increased risk fortype 2 diabetes. (See, e.g., Grant et al., Nature Genetics, 38(3):320-323 (2006)). Likewise, mutations in the recognition sequence ofbinding proteins have also been shown to be associated with diseases anddisorders, such as a SNP within the promoter of human coagulation factorVII leading to an inability of Specificity Protein 1 (Sp1) to bind,which results in a severe bleeding disorder. (See, Carew et al., “SevereFactor VII Deficiency Due to a Mutation Disrupting an Spl Binding Sitein the Factor VII Promoter,” Blood, 92: 1639-1645 (1998)). Thus, in thecontinuing quest to personalize medical diagnostics and therapies to thespecific individual being treated, there is a need for improved methodsto measure the binding affinities of binding proteins based upon theindividual's personal genome so that diagnoses and therapies can beadjusted accordingly. Analysis of an individual's particular bindingaffinities between various binding proteins and their relevantrecognition sites can further explain the genetic contribution to avariety of medical conditions when knowledge of the mutation alone isinsufficient to determine and implement a therapy that is personalizedto the individual.

BRIEF SUMMARY OF THE INVENTION

Various embodiments of the disclosed assay fulfill the need for improvedassays to measure the affinity of binding proteins for their recognitionsites, particularly the need for assays which are personalized to anindividual, including some embodiments which incorporate both nucleicacid sequences and binding proteins specific to the individual ofinterest. In general, the disclosed methods and kits are directed tomeasuring an affinity level of at least one binding protein for at leastone recognition site.

Certain embodiments begin with a capture oligonucleotide attached to asubstrate, where the capture oligonucleotide includes a portion that iscomplementary to a target nucleic acid sequence. Captureoligonucleotides may be DNA or RNA, or analogs thereof, and of varioussequence lengths depending upon the embodiment, including ranges from 10to 100 nucleotides, and attached to the substrate at either their 5′ or3′ end. Capture oligonucleotides may synthesized in situ on thesubstrate or may be attached to the substrate after synthesis. Thesubstrate and array can be in any suitable format, including spotted andin situ synthesized microarrays, liquid arrays, inkjet arrays, and beadarrays. The portion of the capture oligonucleotides that iscomplementary to the target nucleic acid sequence will vary in lengthdepending upon the desired characteristics of the assay and thetechnique utilized to create the capture oligonucleotides. The targetnucleic acid sequence may be from any organism of interest, eukaryoticor prokaryotic, including a human individual such as a patient.Utilization of a specific individual to provide the genetic materialupon which the target sequence is extracted or based upon allowscustomization of the target sequences within the assay to includewhatever mutations, such as SNPS, that may be present in the sourceindividual. Various processing and preparation techniques of the sampleand the target sequences may be utilized according to differentembodiments. When the target sequences are in a suitable condition forhybridization, they are introduced to the substrate and allowed tohybridize with the capture oligonucleotides present.

Certain embodiments will then synthesize a strand that is complementaryto the target sequence. In some embodiments, this may occurenzymatically through extension of the capture oligonucleotide with apolymerase until a double-stranded oligonucleotide is formed with thetarget sequence and the extended capture oligonucleotide. Otherembodiments will not create or retain double-stranded oligonucleotides,as certain nucleic acid binding proteins are specific to single-strandedDNA or RNA. Whether the resulting oligonucleotide is double-stranded orsingle-stranded, it desirably includes a recognition site, comprising arecognition sequence, for a binding protein. The identity and length ofthe recognition sequence will depend upon the particular binding proteinof interest.

Embodiments will then introduce one or more binding proteins and allowthem to potentially bind to the one or more recognition sites which maybe present. Multiple binding proteins may be utilized within an assay,such as a wild type binding protein and one or more mutant variants.Binding proteins may be obtained from commercial sources, orpreferentially translated based upon the genetic material of theindividual of interest, such as through in vitro recombinanttranslation. Within certain embodiments, the binding proteins at issuemay require or desirably involve activation, modification, etc. beforethe assay continues. Such adjustments to the binding proteins mayinclude, e.g., phosphorylation, acetylation or methylation, depending onthe particular binding protein of interest.

Translation and use of binding proteins specific to the individual ofinterest allows any mutations present in the binding protein to beaccounted for within the assay. Embodiments which utilize geneticmaterial from an individual of interest to obtain or produce the targetnucleic acid sequences and binding proteins to be utilized within theassay produce binding affinity measurements which are entirely specificto the individual of interest. The binding proteins may be eitherdirectly or indirectly labeled, such as with fluorescent labels.Antibodies may also be utilized within the labeling strategy in someembodiments. In some embodiments, each different type of binding proteinmay have a distinguishable label or combination of labels. Detection ofthe relevant labels allows the assay to measure the affinity level ofthe one or more binding proteins of interest for one or more recognitionsites of interest. The measured affinity level may be in terms ofabsolute and/or relative quantification, depending on the label(s)utilized, the configuration of the assay, the manner of detection (e.g.,excitation and observation of fluorescent emissions from differentfluorophores), etc.

In certain embodiments, the assay includes capture oligonucleotides inwhich the complementary portion, which hybridizes with the targetnucleic acid sequence, is a unique sequence. In other embodiments, thecomplementary portion is a unique, conserved sequence. The captureoligonucleotide may also include additional portions, such as anidentification portion comprising a unique sequence. Depending upon theembodiment, one or more substrates may be utilized within a singleassay, and each substrate may have one or more capture oligonucleotides.Each substrate may have attached only a single type of captureoligonucleotide, or may have multiple different capture oligonucleotidesattached. In certain embodiments, a pair of capture oligonucleotides maybe utilized for each target nucleic acid sequence, where each of the twocapture oligonucleotides hybridizes to a different portion of the targetnucleic acid sequence. The substrate itself may also comprise additionalcomponents, such as detectable, pre-determined code built into thesubstrate that allows a particular substrate to be distinguished fromother substrates that may be used within the same assay.

Certain embodiments incorporate the use of Molecular Inversion Probe(MIP) technology upstream of the binding protein affinity portion of theassay. MIP probes comprise at least two regions for cooperativehybridization with a target that facilitates circularization of theprobe after hybridization, as well as other portions utilized withinvarious embodiments for functionalities such as cleavage of thecircularized probe, amplification through the use of primer bindingsites, and the incorporation of unique tag sequences within amplicons.Various embodiments utilize MIP probes to selective enrich a nucleicacid sample for specific targets, while using the cooperativehybridization aspect of the probes to ensure high specificity whileallowing for any mutations present within the recognition sequences ofthe recognition sites at issue to be incorporated within the amplicons.MIP probes enable many embodiments to carefully select the recognitionsites from precise locations within the genome to ensure that thebinding protein affinity portion of the assay is performed with respectto the recognition site of interest, and not with respect to adifference occurrence of the relevant recognition sequence within thesample.

The above embodiments are not necessarily inclusive or exclusive of eachother and may be combined in any manner that is non-conflicting andotherwise possible, whether they be presented in association with asame, or a different, aspect or embodiment. The description of oneembodiment is not generally intended to be limiting with respect toother embodiments. Also, any one or more function, step, operation, ortechnique described elsewhere in this specification may, in alternativeembodiments, be combined with any one or more function, step, operation,or technique described in the summary. Thus, the above embodiments areillustrative rather than limiting.

BRIEF DESCRIPTION OF THE DRAWINGS

The above and further features will be more clearly appreciated from thefollowing detailed description when taken in conjunction with theaccompanying drawings. In functional block diagrams, rectanglesgenerally indicate functional elements and parallelograms generallyindicate data. In method flow charts, rectangles generally indicatemethod steps and diamond shapes generally indicate decision elements.All of these conventions, however, are intended to be typical orillustrative, rather than limiting.

FIG. 1(A) illustrates a non-limiting example of capture of a targetfragment with a capture oligonucleotide that is attached to a solidsupport.

FIG. 1(B) illustrates a non-limiting example of extension of the captureoligonucleotide based upon the target fragment captured in FIG. 1(A),thus forming a double-stranded protein binding site.

FIG. 1(C) illustrates a non-limiting example of binding of a labeledbinding protein to the double-stranded protein binding site formed inFIG. 1(B).

FIG. 2(A) illustrates a non-limiting example of cooperative capture of atarget fragment with two different capture oligonucleotides that areattached to a solid support.

FIG. 2(B) illustrates a non-limiting example of extension of one of thecapture oligonucleotides based upon the target fragment captured in FIG.2(A), thus forming a double-stranded protein binding site.

FIG. 2(C) illustrates a non-limiting example of binding of a labeledbinding protein to the double-stranded binding site formed in FIG. 2(B).

FIG. 3 illustrates a non-limiting example of Molecular Inversion Probe(MIP) technology as utilized within a MIP probe that begins in a linearform, is circularized after hybridization to a target nucleic acid, andis subsequently linearized.

FIG. 4(A) illustrates a non-limiting example of a MIP probe in aninitial, linear form.

FIG. 4(B) illustrates a non-limiting example of the MIP probe from FIG.4(A) after cooperative hybridization of its two different genomichomology regions to a target nucleic acid.

FIG. 4(C) illustrates a non-limiting example of the MIP probe from FIG.4(B) in circularized form after filling of the gap between the twogenomic homology regions to form a single, combined genomic homologyregion.

FIG. 4(D) illustrates a non-limiting example of the MIP probe from FIG.4(C) after linearization effected by separation of the MIP probe fromthe target nucleic acid and cleavage of the circularized MIP probe forre-linearization.

DETAILED DESCRIPTION I. General Description

Reference will now be made in detail to exemplary embodiments of theinvention. While the invention will be described in conjunction with theexemplary embodiments, it will be understood that they are not intendedto limit the invention to these embodiments. On the contrary, theinvention is intended to encompass alternatives, modifications andequivalents, which may be included within the spirit and scope of theinvention.

The invention relates to diverse fields impacted by the nature ofmolecular interaction, including chemistry, biology, medicine anddiagnostics. The invention described herein has many embodiments andrelies on many patents, applications and other references for detailsknown to those of the art. Therefore, when a patent, application, orother reference is cited or repeated below, it should be understood thatthe entire disclosure of the document cited is incorporated by referencein its entirety for all purposes as well as for the proposition that isrecited. All documents, e.g., publications and patent applications,cited in this disclosure, including the foregoing, are incorporatedherein by reference in their entireties for all purposes to the sameextent as if each of the individual documents were specifically andindividually indicated to be so incorporated herein by reference in itsentirety.

As used in this application, the singular form “a,” “an,” and “the”include plural references unless the context clearly dictates otherwise.For example, the term “an agent” includes a plurality of agents,including mixtures thereof.

An individual is not limited to a human being but may also be otherorganisms including, but not limited to, mammals, plants, bacteria, orcells derived from any of the above.

Throughout this disclosure, various aspects of this invention can bepresented in a range format. It should be understood that when adescription is provided in range format, this is merely for convenienceand brevity and should not be construed as an inflexible limitation onthe scope of the invention. Accordingly, the description of a rangeshould be considered to have specifically disclosed all the possiblesub-ranges as well as individual numerical values within that range. Forexample, description of a range such as from 1 to 6 should be consideredto have specifically disclosed sub-ranges such as from 1 to 3, from 1 to4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6, for example, aswell as individual numbers within that range, for example, 1, 2, 3, 4,5, and 6. This applies regardless of the breadth of the range.

The practice of the invention described herein may employ, unlessotherwise indicated, conventional techniques and descriptions of organicchemistry, polymer technology, molecular biology (including recombinanttechniques), cell biology, biochemistry, and immunology, which arewithin the skill of one of skill in the art. Such conventionaltechniques include polymer array synthesis, hybridization, ligation, anddetection of hybridization using a detectable label. Specificillustrations of suitable techniques are provided by reference to theexamples hereinbelow. However, other equivalent conventional proceduresmay also be employed. Such conventional techniques and descriptions maybe found in standard laboratory manuals, such as Genome Analysis: ALaboratory Manual Series (Vols. I-IV), Using Antibodies: A LaboratoryManual, Cells: A Laboratory Manual, PCR Primer: A Laboratory Manual, andMolecular Cloning: A Laboratory Manual (all from Cold Spring HarborLaboratory Press), Stryer, L. (1995), Biochemistry, 4th Ed., Freeman,New York, Gait, Oligonucleotide Synthesis: A Practical Approach, (1984),IRL Press, London, Nelson and Cox (2000), Lehninger, Principles ofBiochemistry, 3^(rd) Ed., W.H. Freeman Pub., New York, N.Y., and Berg etal. (2002), Biochemistry, 5^(th) Ed., W.H. Freeman Pub., New York, N.Y.,all of which are herein incorporated in their entirety by reference forall purposes.

The invention may employ solid substrates, including arrays in someembodiments. Methods and techniques applicable to polymer (includingprotein) array synthesis have been described in U.S. Ser. No. 09/536,841(abandoned), WO 00/58516, U.S. Pat. Nos. 5,143,854, 5,242,974,5,252,743, 5,324,633, 5,384,261, 5,405,783, 5,424,186, 5,451,683,5,482,867, 5,491,074, 5,527,681, 5,550,215, 5,571,639, 5,578,832,5,593,839, 5,599,695, 5,624,711, 5,631,734, 5,795,716, 5,831,070,5,837,832, 5,856,101, 5,858,659, 5,936,324, 5,968,740, 5,974,164,5,981,185, 5,981,956, 6,025,601, 6,033,860, 6,040,193, 6,090,555,6,136,269, 6,269,846 and 6,428,752, and in PCT Applications Nos.PCT/US99/00730 (International Publication No. WO 99/36760) andPCT/US01/04285 (International Publication No. WO 01/58593), which areall incorporated herein by reference in their entirety for all purposes.

Patents that describe synthesis techniques in specific embodimentsinclude U.S. Pat. Nos. 5,412,087, 6,147,205, 6,262,216, 6,310,189,5,889,165, and 5,959,098. Nucleic acid arrays are described in many ofthe above patents, but the same techniques are applied to polypeptidearrays.

Nucleic acid arrays that are useful in the described invention include,but are not limited to, those that are commercially available fromAffymetrix (Santa Clara, Calif.) under the brand name GENECHIP®.

Many uses for polymers attached to solid substrates are contemplatedherein. These uses include, but are not limited to, gene expressionmonitoring, profiling, library screening, genotyping and diagnostics.Methods of gene expression monitoring and profiling are described inU.S. Pat. Nos. 5,800,992, 6,013,449, 6,020,135, 6,033,860, 6,040,138,6,177,248 and 6,309,822. Genotyping methods, and uses thereof, aredisclosed in U.S. patent application Ser. No. 10/442,021 (abandoned) andU.S. Pat. Nos. 5,856,092, 6,300,063, 5,858,659, 6,284,460, 6,361,947,6,368,799, 6,333,179, and 6,872,529. Other uses are described in U.S.Pat. Nos. 5,871,928, 5,902,723, 6,045,996, 5,541,061, and 6,197,506.

Also contemplated are sample preparation methods in certain embodiments.Prior to, or concurrent with, genotyping, the genomic sample may beamplified by a variety of mechanisms, some of which may employ PCR.(See, for example, PCR Technology: Principles and Applications for DNAAmplification, Ed. H.A. Erlich, Freeman Press, NY, N.Y., 1992; PCRProtocols: A Guide to Methods and Applications, Eds. Innis, et al.,Academic Press, San Diego, Calif., 1990; Mattila et al., Nucleic AcidsRes., 19:4967, 1991; Eckert et al., PCR Methods and Applications, 1:17,1991; PCR, Eds. McPherson et al., IRL Press, Oxford, 1991; and U.S. Pat.Nos. 4,683,202, 4,683,195, 4,800,159 4,965,188, and 5,333,675, each ofwhich is incorporated herein by reference in their entireties for allpurposes. The sample may also be amplified on the array. (See, forexample, U.S. Pat. No. 6,300,070 and U.S. patent application Ser. No.09/513,300 (abandoned), all of which are incorporated herein byreference).

Other suitable amplification methods include the ligase chain reaction(LCR) (see, for example, Wu and Wallace, Genomics, 4:560 (1989),Landegren et al., Science, 241:1077 (1988) and Barringer et al., Gene,89:117 (1990)), transcription amplification (Kwoh et al., Proc. Natl.Acad. Sci. USA, 86:1173 (1989) and WO 88/10315), self-sustained sequencereplication (Guatelli et al., Proc. Nat. Acad. Sci. USA, 87:1874 (1990)and WO 90/06995), selective amplification of target polynucleotidesequences (U.S. Pat. No. 6,410,276), consensus sequence primedpolymerase chain reaction (CP-PCR) (U.S. Pat. No. 4,437,975),arbitrarily primed polymerase chain reaction (AP-PCR) (U.S. Pat. Nos. 5,413,909 and 5,861,245) and nucleic acid based sequence amplification(NABSA). (See also, U.S. Pat. Nos. 5,409,818, 5,554,517, and 6,063,603,each of which is incorporated herein by reference). Other amplificationmethods that may be used are described in, for instance, U.S. Pat. Nos.6,582,938, 5,242,794, 5,494,810, and 4,988,617, each of which isincorporated herein by reference.

Additional methods of sample preparation and techniques for reducing thecomplexity of a nucleic sample are described in Dong et al., GenomeResearch, 11:1418 (2001), U.S. Pat. Nos. 6,361,947, 6,391,592,6,632,611, 6,872,529 and 6,958,225, and in U.S. patent application Ser.No. 09/916,135 (abandoned).

Methods for conducting polynucleotide hybridization assays have beenwell developed in the art. Hybridization assay procedures and conditionswill vary depending on the application and are selected in accordancewith known general binding methods, including those referred to inManiatis et al., Molecular Cloning: A Laboratory Manual, 2^(nd) Ed.,Cold Spring Harbor, N.Y, (1989); Berger and Kimmel, Methods inEnzymology, Guide to Molecular Cloning Techniques, Vol. 152, AcademicPress, Inc., San Diego, Calif. (1987); Young and Davism, Proc. Nat'l.Acad. Sci., 80:1194 (1983). Methods and apparatus for performingrepeated and controlled hybridization reactions have been described in,for example, U.S. Pat. Nos. 5,871,928, 5,874,219, 6,045,996, 6,386,749,and 6,391,623 each of which are incorporated herein by reference.

The invention also provides signal detection of hybridization betweenligands in certain embodiments. (See, U.S. Pat. Nos. 5,143,854,5,578,832, 5,631,734, 5,834,758, 5,936,324, 5,981,956, 6,025,601,6,141,096, 6,185,030, 6,201,639, 6,218,803, and 6,225,625, U.S. patentapplication Ser. No. 10/389,194 (U.S. Patent Application Publication No.2004/0012676, allowed) and PCT Application PCT/US99/06097 (published asWO 99/47964), each of which is hereby incorporated by reference in itsentirety for all purposes).

The practice of the inventions herein may also employ conventionalbiology methods, software and systems. Computer software products of theinvention typically include, for instance, computer readable mediumhaving computer-executable instructions for performing the logic stepsof the method of the invention. Suitable computer readable mediuminclude, but are not limited to, a floppy disk, CD-ROM/DVD/DVD-ROM,hard-disk drive, flash memory, ROM/RAM, magnetic tapes, and others thatmay be developed. The computer executable instructions may be written ina suitable computer language or combination of several computerlanguages. Basic computational biology methods which may be employed inthe invention are described in, for example, Setubal and Meidanis etal., Introduction to Computational Biology Methods, PWS PublishingCompany, Boston, (1997); Salzberg, Searles, Kasif, (Ed.), ComputationalMethods in Molecular Biology, Elsevier, Amsterdam, (1998); Rashidi andBuehler, Bioinformatics Basics: Application in Biological Science andMedicine, CRC Press, London, (2000); and Andreas D. Baxevanis and B. F.Francis Ouellette, Bioinformatics: A Practical Guide to the Analysis ofGene and Proteins, Wiley-Interscience, 2^(nd) ed., (2001); and also U.S.Pat. No. 6,420,108.

The invention may also make use of various computer program products andsoftware for a variety of purposes, such as probe design, management ofdata, analysis, and instrument operation. (See, e.g., U.S. Pat. Nos.5,593,839, 5,795,716, 5,733,729, 5,974,164, 6,066,454, 6,090,555,6,185,561, 6,188,783, 6,223,127, 6,229,911 and 6,308,170).

Additionally, the invention encompasses embodiments that may includemethods for providing genetic information over networks such as theinternet, as disclosed in, for instance, U.S. patent application Ser.Nos. 10/197,621 (U.S. Patent Application Publication No. 20030097222),10/063,559 (U.S. Patent Application Publication No. 20020183936,abandoned), 10/065,856 (U.S. Patent Application Publication No.20030100995, abandoned), 10/065,868 (U.S. Patent Application PublicationNo. 20030120432, abandoned), 10/328,818 (U.S. Patent ApplicationPublication No. 20040002818, abandoned), 10/328,872 (U.S. PatentApplication Publication No. 20040126840, abandoned), 10/423,403 (U.S.Patent Application Publication No. 20040049354, abandoned), and60/482,389 (expired).

II. Definitions of Selected Terms

The term “array” as used herein refers to an intentionally createdcollection of nucleic acids which can be prepared either syntheticallyor biosynthetically and screened for biological activity in a variety ofdifferent formats (e.g., libraries of soluble molecules; and librariesof oligos tethered to resin beads, silica chips, or other solidsupports). The molecules in the array can be identical or different fromeach other. Additionally, the term “array” is meant to include thoselibraries of “nucleic acids” which can be prepared by spotting nucleicacids of essentially any length (e.g., from 1 to about 1000 nucleotidemonomers in length) onto a substrate.

The term “binding protein” as used herein refers to a protein which haseither a specific or general binding affinity for nucleic acids. Thenucleic acids may be either DNA or RNA, and additionally may be eithersingle-stranded or double-stranded. These binding proteins may interactthrough any possible mechanism, with non-limiting examples beinginteraction through the major groove or the minor groove. Bindingproteins include at least one binding domain, a portion of the proteinthat recognizes single-stranded or double-stranded DNA or RNA, eitherspecifically or non-specifically. If a binding protein has specificbinding properties, then the binding protein will preferentially bind toone or more “recognition sites,” defined separately herein, dependingupon the corresponding “recognition sequence” or “recognitionsequences,” also defined separately herein, for which the binding domainof a binding protein will recognize for further interaction and binding.Binding proteins may also be associated with one or more accessorymolecules, such as cofactor proteins, which may affect the bindingaffinity which a particular binding protein possesses for a recognitionsite. Binding proteins may additionally be associated with one or moresteps to activate or otherwise modify the binding protein before certainsteps within the assay. Non-limiting examples of such activation ormodification steps include phosphorylation, acetylation and methylation.

The term “capture oligonucleotide” as used herein refers to an“oligonucleotide,” defined separately herein, utilized in capturing atarget fragment. Capture oligonucleotides may be any form of “nucleicacid” as defined herein. The length of capture oligonucleotide will varydepending upon the particular embodiment, the length of the targetfragment, the length of the “recognition sequence” of the “recognitionsite.” Non-limiting examples of the length for capture oligonucleotidesinclude between 10 and 100 nucleotides, for example, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 60, 75 or 90nucleotides. Other lengths within this range, as well as shorter andlonger lengths (e.g., 8, 9, 105, 110) are also possible depending uponthe embodiment. One or more capture oligonucleotides may be utilizedwith respect to a single recognition site (e.g., a first and secondcapture oligonucleotide). Many embodiments include one or more captureoligonucleotides attached to one or more substrates, wherein attachmentincludes, for instance, attaching pre-synthesized captureoligonucleotides to the substrate or in situ synthesis of the captureoligonucleotides. Depending upon the embodiment, a single substrate mayhave one or more copies of one or more particular captureoligonucleotides. Other embodiments, however, do not attach captureoligonucleotides to substrates.

The term “complementary” as used herein refers to the hybridization orbase pairing between nucleotides or nucleic acids, such as, forinstance, between the two strands of a double stranded DNA molecule orbetween an oligonucleotide primer and a primer binding site on a singlestranded nucleic acid to be sequenced or amplified. Complementarynucleotides are, generally, A and T (or A and U), or C and G. Two singlestranded RNA or DNA molecules are said to be complementary when thenucleotides of one strand, optimally aligned and compared and withappropriate nucleotide insertions or deletions, pair with at least about80% of the nucleotides of the other strand, usually at least about 90%to 95%, and more preferably from about 98 to 100%. Alternatively,complementarity exists when an RNA or DNA strand will hybridize underselective hybridization conditions to its complement. Typically,selective hybridization will occur when there is at least about 65%complementary over a stretch of at least 14 to 25 nucleotides,preferably at least about 75%, more preferably at least about 90%complementary. See, M. Kanehisa Nucleic Acids Res. 12:203 (1984),incorporated herein by reference.

The term “complementary fragment” as used herein refers to acomplementary nucleic acid strand that is synthesized in order to makethe “target fragment,” defined separately herein, double-stranded. Thecomplementary fragment may be made through any viable method. Anon-limiting example is enzymatically through the use of a DNApolymerase. The length and identity of the nucleotides at each positionof the complementary fragment depend upon the length and sequenceidentity of the target fragment. Furthermore, a complementary fragmentis not required for all embodiments, as binding proteins which arespecific for single-stranded recognition sites may not bind if therecognition site has been made double-stranded through the synthesis ofa complementary fragment. However, a complementary fragment may still beutilized in embodiments directed at single-stranded binding proteins. Anon-limiting example of such a use would be the creation of asingle-stranded recognition site through extension of the captureoligonucleotide, subsequent separation of the strands, and removal ofthe single-stranded target fragment to free the recognition site on thestrand containing the capture oligonucleotide and the complementaryfragment for possible binding.

The term “complementary region” or “complementary portion” as usedherein refers to one or more regions of nucleotides of one or morecapture oligonucleotides that are complementary to a target fragment.The number of complementary regions generally, but not necessarily,equals the number of capture oligonucleotides associated with aparticular recognition site (e.g., if two capture oligonucleotides areutilized to capture a particular target fragment, there will generallybe at least two complementary regions). The complementary region may be,but is not required to be, a unique sequence with respect to the genomeof the sample at issue or the processed sample (which may have a lowercomplexity than the overall genome due to complexity reduction,selective amplification, etc.). The complementary region may also be aunique, conserved sequence. The length of the complementary region willdepend upon the embodiment and factors such as the desired specificity.The complementary region may be, for example, from 10 to 100 nucleotidesin length (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35,40, 45, 50, 60, 75 or 90 nucleotides). Other lengths within this range,as well as shorter and longer lengths (e.g., 8, 9, 105, 110) are alsopossible depending upon the embodiment.

The term “genome” as used herein is all the genetic material in thechromosomes of an organism. DNA derived from the genetic material in thechromosomes of a particular organism is genomic DNA. A genomic libraryis a collection of clones made from a set of randomly generatedoverlapping DNA fragments representing the entire genome of an organism.

The term “hybridization conditions” as used herein will typicallyinclude salt concentrations of less than about 1 M, more usually lessthan about 500 mM and preferably less than about 200 mM. Hybridizationtemperatures can be as low as 5° C., but are typically greater than 22°C., more typically greater than about 30° C., and preferably in excessof about 37° C. Longer fragments may require higher hybridizationtemperatures for specific hybridization. As other factors may affect thestringency of hybridization, including base composition and length ofthe complementary strands, presence of organic solvents and extent ofbase mismatching, the combination of parameters is more important thanthe absolute measure of any one alone.

The term “hybridization” as used herein refers to the process in whichtwo single-stranded polynucleotides bind non-covalently to form a stabledouble-stranded polynucleotide; triple-stranded hybridization is alsotheoretically possible. The resulting (usually) double-strandedpolynucleotide is a “hybrid.” The proportion of the population ofpolynucleotides that forms stable hybrids is referred to herein as the“degree of hybridization.” Hybridizations are usually performed understringent conditions, for example, at a salt concentration of no morethan 1 M and a temperature of at least 25° C. For example, conditions of5×SSPE (750 mM NaCl, 50 mM NaPhosphate, 5 mM EDTA, pH 7.4) and atemperature of 25-30° C. are suitable for allele-specific probehybridizations. For stringent conditions, see, for example, Sambrook,Fritsche and Maniatis, “Molecular Cloning A laboratory Manual” 2^(nd)Ed. Cold Spring Harbor Press (1989), which is hereby incorporated byreference in its entirety for all purposes above. Hybridizations, e.g.,allele-specific probe hybridizations, are generally performed understringent conditions. For example, conditions where the saltconcentration is no more than about 1 Molar (M) and a temperature of atleast 25° C., e.g., 750 mM NaCl, 50 mM Sodium Phosphate, 5 mM EDTA, pH7.4 (5×SSPE) and a temperature of from about 25 to about 30° C.

The term “hybridizing specifically to” as used herein refers to thebinding, duplexing, or hybridizing of a molecule only to a particularnucleotide sequence or sequences under stringent conditions when thatsequence is present in.

The term “label” as used herein refers to a molecule or combination ofmolecules which facilitate detection of a binding protein or a nucleicacid. The label may be a detectable chemical or biochemical moiety or asignal obtained from an enzyme-linked assay. The label molecule(s) canbe applied directly to the label target or indirectly through the use oftwo or more sets of molecules, antibodies, etc. Non-limiting examples offluorescent labels include organic dyes, biological fluorophores, andquantum dots. Labels may include the use of antibodies. Non-limitingexamples of antibody labeling techniques include radioisotopes,enzymatic tags, and fluorescent tags.

The term “mutation” or “polymorphism” as used herein refers to theoccurrence of two or more genetically determined alternative sequencesor alleles in a population. A polymorphic marker or site is the locus atwhich divergence occurs. A mutation may comprise one or more basechanges, an insertion, a repeat, or a deletion. Larger mutations maycomprise one or more amplifications or duplications, deletions,translocations, interstitial deletions, inversions, or a loss ofheterozygosity with respect to chromosomal structural. A polymorphiclocus may be as small as one base pair. Polymorphic markers includerestriction fragment length polymorphisms, variable number of tandemrepeats, hypervariable regions, minisatellites, dinucleotide repeats,trinucleotide repeats, tetranucleotide repeats, simple sequence repeats,and insertion elements such as Alu. The first identified allelic form isarbitrarily designated as the reference form and other allelic forms aredesignated as alternative or variant alleles. The allelic form occurringmost frequently in a selected population is sometimes referred to as thewildtype form. Diploid organisms may be homozygous or heterozygous forallelic forms. A diallelic polymorphism has two forms. A triallelicpolymorphism has three forms. Single nucleotide polymorphisms (SNPs) areincluded in polymorphisms.

The term “nucleic acid” or “nucleic acids” as used herein refers to apolymeric form of nucleotides of any length, for exampleribonucleotides, deoxyribonucleotides, locked nucleic acids (LNAs) orpeptide nucleic acids (PNAs), that comprise purine and pyrimidine bases,or other natural, chemically or biochemically modified, non-natural, orderivatized nucleotide bases. The backbone of the polynucleotide cancomprise sugars and phosphate groups, as may typically be found in RNAor DNA, or modified or substituted sugar or phosphate groups. Apolynucleotide may comprise modified nucleotides, such as methylated,hydroxymethylated or glucosylated nucleotides and nucleotide analogs.The sequence of nucleotides may be interrupted by non-nucleotidecomponents. Thus the terms nucleoside, nucleotide, deoxynucleoside anddeoxynucleotide generally include analogs such as those describedherein. These analogs are those molecules having some structuralfeatures in common with a naturally occurring nucleoside or nucleotidesuch that when incorporated into a nucleic acid or oligonucleosidesequence, they allow hybridization with a naturally occurring nucleicacid sequence in solution. Typically, these analogs are derived fromnaturally occurring nucleosides and nucleotides by replacing and/ormodifying the base, the ribose or the phosphodiester moiety. The changescan be tailor made to stabilize or destabilize hybrid formation orenhance the specificity of hybridization with a complementary nucleicacid sequence as desired.

The term “oligonucleotide” or “polynucleotide,” as used interchangeablyherein, refers to a nucleic acid ranging from at least 2, preferably atleast 8, and more preferably at least 15 nucleotides in length or acompound that specifically hybridizes to a polynucleotide.Polynucleotides of the invention include sequences of deoxyribonucleicacid (DNA) or ribonucleic acid (RNA) which may be isolated from naturalsources, recombinantly produced or artificially synthesized and mimeticsthereof. A further example of a polynucleotide of the invention may belocked nucleic acids (LNAs) or peptide nucleic acid (PNA). The inventionalso encompasses situations in which there is a nontraditional basepairing such as Hoogsteen base pairing which has been identified incertain tRNA molecules and postulated to exist in a triple helix.

The term “primer” as used herein refers to a single-strandedoligonucleotide capable of acting as a point of initiation fortemplate-directed DNA synthesis under suitable conditions e.g., bufferand temperature, in the presence of four different nucleosidetriphosphates and an agent for polymerization, such as, for example, DNAor RNA polymerase or reverse transcriptase. The length of the primer, inany given case, depends on, for example, the intended use of the primer,and generally ranges from 15 to 30 nucleotides. Short primer moleculesgenerally require cooler temperatures to form sufficiently stable hybridcomplexes with the template. A primer need not reflect the exactsequence of the template but must be sufficiently complementary tohybridize with such template. The primer site or primer binding site isthe area of the template to which a primer hybridizes. The primer pairis a set of primers including a 5′ upstream primer that hybridizes withthe 5′ end of the sequence to be amplified and a 3′ downstream primerthat hybridizes with the complement of the 3′ end of the sequence to beamplified.

The term “recognition sequence” as used herein refers to the sequence ofDNA or RNA for which the binding domain of a binding protein may exhibitbinding specificity. A recognition sequence is the sequence or sequencesof nucleotides recognized by the binding domain of the particularprotein, with the number and identity of the nucleotides within thesequence dependent upon the binding protein at issue. Thus, somerecognition sequences will be shorter (e.g., 6 nucleotides) in lengththan others (e.g., 15 nucleotides), but it should be appreciated thatthe length and identity of any recognition sequence depends upon the oneor more binding domains of the binding protein at issue. While someproteins may exhibit binding that is specific to only one particularrecognition sequence, other binding proteins may bind to a plurality ofrecognition sequences. The plurality of recognition sequences may differin any number of ways, such as smaller changes consisting of a singlebase change (e.g., a binding protein associated with two recognitionsequences that contain either a guanine or thymine at a particularposition), or larger changes (e.g., a change in the number ofnucleotides in the sequence and a change in the identity of two or morebases).

The term “recognition site” as used herein refers to the location withinthe DNA or RNA sequence(s) where a recognition sequence is located.Depending upon the length of the sequence(s) at issue, and the lengthand identity of the recognition sequence, a particular recognitionsequence may occur at more than one recognition site. Furthermore, if abinding protein is capable of binding to a plurality of recognitionsequences (e.g., a binding protein which will bind to any of threerecognition sequences which differ in length and/or identity of bases),there may be one or more recognition sites for that binding proteinwithin a particular sequence(s) of DNA or RNA.

The term “sample” as used refers to any collection of nucleic acids. Asample may contain only desired nucleic acids, such as desired targetfragments, or may additionally contain undesired nucleic acids as wellas non-nucleic acid molecules. Non-limiting examples of samples includetotal genomic DNA, total RNA or total mRNA. Additionally, samples mayhave their complexity reduced, such as by fragmentation followed byadaptor ligation and amplification of the fragments. Moreover, a sampleof nucleic acids may have been enriched for a given population but maystill include other undesirable populations. For example, a sample ofnucleic acids may be enriched for a desired set of DNA sequences but maystill include some undesired DNA sequences. A sample may be from anyparticular organism, eukaryotic or prokaryotic. Non-limiting examples oforganisms include humans, chimpanzees, dogs, rats, Saccharomycescerevisiae, and Escherichia coli. Furthermore, a sample may be from anindividual organism, a collection of organisms, or recombinantly orartificially produced.

The term “single-nucleotide polymorphism” (“SNP”) as used herein refersto a DNA sequence variation occurring when a single nucleotide—A, T, C,or G—in the genome (or other shared sequence) differs between members ofa species (or between paired chromosomes in an individual). For example,two sequenced DNA fragments from different individuals, AAGCCTA toAAGCTTA, contain a difference in a single nucleotide. In this case wesay that there are two alleles: C and T.

The term “substrate” as used herein refers to a material or group ofmaterials having a rigid or semi-rigid surface or surfaces. In someembodiments, at least one surface of the solid support will besubstantially flat, although in some embodiments it may be desirable tophysically separate synthesis regions for different compounds with, forexample, wells, raised regions, pins, etched trenches, or the like.According to various embodiments, the solid support(s) will also takethe form of, for example, wafers, chips, beads, resins, gels,microspheres, microparticles, slides, or other geometric configurations.Any suitable material(s) may be used for the substrate, includingbiological, non-biological, organic, and inorganic materials, or anycombination of these. Non-limiting examples of materials for substratesinclude but are not limited to Si, Ge, GeAs, GaP, SiO₂, SiN₄, othersilicon based materials, glass, fused silica, fused quartz,polyvinylidene fluoride, polycarbonate, other polymers, combinations ofthese, and other suitable materials known in the art

The term “target fragment” or “target nucleic acid sequence” or “targetsequence” as used interchangeably herein refers to a nucleic acidsequence which contains one or more regions or portions that arecomplementary to at least one capture oligonucleotide. Non-limitingexamples include a nucleic acid containing a single region which iscomplementary to a specific capture oligonucleotide, and a nucleic acidwhich contains two complementary regions, each of which is complementaryto a different capture oligonucleotide. The length of the targetfragment may be any suitable size, but preferably includes, in additionto the one or more complementary portions, the entirety of a recognitionsite, such that all of the nucleotides of that recognition site'srecognition sequence are included within the target fragment, or withinthe complement of the target fragment. A sample, however, may containundesired target fragments which do not contain the desired recognitionsite, or only contain a portion of the desired recognition site'srecognition sequence.

III. Biological Microarrays

A biological microarray often includes nucleic acid oligonucleotideprobes that are used to extract information related to, for example,various nucleic acid samples, and other related substances of interest,such as nucleic acid binding proteins. The nucleic acid samples areexposed to the nucleic acid probes under certain conditions that allowhybridization. The sample nucleic acids may be labeled with a detectablechemical moiety, such as a fluorescent dye, or signal obtained from anenzyme-linked assay. Additional steps may also be performed beforeprocessing and scanning, depending upon the particular application ofthe microarray and the desired information.

A variety of techniques are known for the creation and use of arrays ofdifferent biological polymers, such as nucleic acid and polypeptidearrays. Many techniques have been commercialized, such as Affymetrix®arrays (Affymetrix, Inc., Santa Clara, Calif.) in the form of GeneChip®array cartridges, array strips, and Axiom® array plates. Othercommercialized arrays include Agilent® arrays (Agilent Technologies,Inc., Santa Clara, Calif.), Illumina® arrays (Illumina, Inc., San Diego,Calif.) and NimbleGen® arrays (Roche NimbleGen, Inc., Madison, Wis.).Such arrays may contain hundreds, thousands, or millions of differentpolynucleotide or polypeptide sequences, depending upon the abilities ofthe particular manufacturing technique at issue with respect to featuresize, the size of the relevant solid support of silicon, glass, or othermaterial, the desired characteristics of the relevant assay, and otherfactors.

A variety of techniques are known for the creation and use of arrays ofdifferent biological polymers, such as nucleic acid and polypeptidearrays. See, e.g., U.S. Pat.No. 5,143,854 to Pirrung et al.; U.S. Pat.No. 5,744,305 to Fodor et al.; U.S. Pat. No. 7,332,273 to Trulson etal.; U.S. Pat. Nos. 5,945,334 and 6,140,044 to Besemer et al.; U.S. Pat.No. 5,545,531 to Rava et al.; U.S. Pat. No. 6,660,233 to Coassin et al.;U.S. Patent Application Publication Nos. 2004/0038388 and 2006/0088863to Yamamoto et al.; U.S. Patent Application Publication No. 2005/0023672to Oostman et al.; U.S. Patent Application Publication No. 2008/0003667to Jones et al.; U.S. Patent Application Publication Nos. 2006/0246576,2006/0234371, 2011/0136699 and 2010/0248981 to Shirazi; pending U.S.patent application Ser. No. 13/157,268, filed Jun. 9, 2011; U.S. Pat.No. 6,242,266 to Schleifer et al.; U.S. Pat. No. 6,375,903 to Cerrina etal.; U.S. Pat. No. 5,436,327 to Southern et al.; U.S. Pat. No. 5,474,796to Brennan; U.S. Pat. No. 5,658,802 to Hayes et al.; U.S. Pat. No.5,770,151 to Roach et al.; U.S. Pat. No. 5,807,522 to Brown et al.; U.S.Pat. No. 5,981,733 to Gamble et al.; U.S. Pat. No. 6,101,946 toMartinsky; U.S. Pat. Nos. 6,355,431 and 6,429,027 to Chee et al.; U.S.Pat. No. 7,510,841 to Stuelpnagel et al., U.S. Pat. Nos. 7,745,091 and7,745,092 to True; U.S. Patent Application Publication No. 2010/0297448to True et al.; and U.S. Patent Application Publication Nos.2010/0227279, 2010/0227770 and 2009/0149340 to True, all of which areexpressly incorporated herein by reference for all purposes.

A non-limiting example of arrays which are suitable for use with certainembodiments include Affymetrix GENECHIP® arrays, which are synthesizedin accordance with techniques sometimes referred to as VLSPS™ (VeryLarge Scale Immobilized Polymer Synthesis) technologies. Some aspects ofVLSPS™ and other microarray manufacturing technologies are described inU.S. Pat. Nos. 5,424,186; 5,143,854; 5,445,934; 5,744,305; 5,831,070;5,837,832; 6,022,963; 6,083,697; 6,291,183; 6,309,831; and 6,310,189,all of which are hereby incorporated by reference in their entiretiesfor all purposes. The probes of these arrays in some implementationsconsist of nucleic acids that are synthesized by methods including thesteps of activating regions of a substrate and then contacting thesubstrate with a selected monomer solution. As used herein, nucleicacids may include any polymer or oligomer of nucleosides or nucleotides(polynucleotides or oligonucleotides) that include pyrimidine and/orpurine bases, preferably cytosine, thymine, and uracil, and adenine andguanine, respectively. Nucleic acids may include anydeoxyribonucleotide, ribonucleotide, and/or peptide nucleic acidcomponent, and/or any chemical variants thereof such as LNAs,methylated, hydroxymethylated or glucosylated forms of these bases, andthe like. The polymers or oligomers may be heterogeneous or homogeneousin composition, and may be isolated from naturally-occurring sources ormay be artificially or synthetically produced. In addition, the nucleicacids may be DNA or RNA, or a mixture thereof, and may exist permanentlyor transitionally in single-stranded or double-stranded form, includinghomoduplex, heteroduplex, and hybrid states. Probes of other biologicalmaterials, such as peptides or polysaccharides as non-limiting examples,may also be formed. For more details regarding possible implementations,see U.S. Pat. No. 6,156,501, which is hereby incorporated by referenceherein in its entirety for all purposes.

A system and method for efficiently synthesizing probe arrays usingmasks is described in U.S. Pat. No. 6,949,638, which is herebyincorporated by reference herein in its entirety for all purposes. Asystem and method for a rapid and flexible microarray manufacturing andonline ordering system is described in U.S. Provisional PatentApplication Ser. No. 60/265,103 (now expired), filed Jan. 29, 2001,which also is hereby incorporated herein by reference in its entiretyfor all purposes. Systems and methods for optical photolithographywithout masks are described in U.S. Pat. No. 6,271,957 and in U.S.patent application Ser. No. 09/683,374 filed Dec. 19, 2001 (nowabandoned), both of which are hereby incorporated by reference herein intheir entireties for all purposes.

The probes of synthesized probe arrays typically are used in conjunctionwith biological target molecules of interest, such as cells, proteins,genes or EST's, other DNA sequences, or other biological elements. Morespecifically, the biological molecule of interest may be a ligand,receptor, peptide, nucleic acid (oligonucleotide or polynucleotide ofRNA or DNA), or any other of the biological molecules listed in U.S.Pat. No. 5,445,934 (incorporated by reference above) at column 5, line66 to column 7, line 51. For example, if transcripts of genes are theinterest of an experiment, the target molecules would be thetranscripts. Other examples include protein fragments and smallmolecules. Target nucleic acid refers to a nucleic acid (often derivedfrom a biological sample) of interest. Frequently, a target molecule isdetected using one or more probes. As used herein, a probe is a moleculefor detecting a target molecule. A probe may be any of the molecules inthe same classes as the target referred to above. As non-limitingexamples, a probe may refer to a nucleic acid, such as anoligonucleotide, capable of binding to a target nucleic acid ofcomplementary sequence through one or more types of chemical bonds,usually through complementary base pairing, usually through hydrogenbond formation. As noted above, a probe may include natural, e.g. A, G,U, C, or T, or modified bases (7-deazaguanosine, inosine, LNA, PNA, forexample). In addition, the bases in probes may be joined by a linkageother than a phosphodiester bond, so long as the bond does not interferewith hybridization. Thus, probes may be peptide nucleic acids in whichthe constituent bases are joined by peptide bonds rather thanphosphodiester linkages. Other examples of probes include antibodiesused to detect peptides or other molecules, any ligands for detectingits binding partners. When referring to targets or probes as nucleicacids, it should be understood that these are illustrative embodimentsthat are not to limit the invention in any way.

The samples or target molecules of interest (hereafter, simply targets)are processed so that, typically, they are spatially associated withcertain probes in the probe array. For example, one or more taggedtargets are distributed over the probe array. In accordance with someimplementations, some targets hybridize with probes and remain at theprobe locations, while non-hybridized targets are washed away. Thesehybridized targets, with their tags or labels, are thus spatiallyassociated with the probes. The hybridized probe and target maysometimes be referred to as a probe-target pair. Detection of thesepairs can serve a variety of purposes, such as to determine whether atarget nucleic acid has a nucleotide sequence identical to or differentfrom a specific reference sequence. (See, for example, U.S. Pat. No.5,837,832, referred to and incorporated above). Other uses include geneexpression monitoring and evaluation (see, e.g., U.S. Pat. No.5,800,992, U.S. Pat. No. 6,040,138, and International Patent App. No.PCT/US98/15151, published as WO99/05323), genotyping (U.S. Pat. No.5,856,092), or other detection of nucleic acids. The '992, '138, and'092 patents, and publication WO99/05323, are incorporated by referenceherein in their entireties for all purposes.

Other techniques exist for depositing probes on a substrate or support.For example, “spotted arrays” are commercially fabricated, typically onmicroscope slides. These arrays consist of liquid spots containingbiological material of potentially varying compositions andconcentrations. For instance, a spot in the array may include a fewstrands of short oligonucleotides in a water solution, or it may includea high concentration of long strands of complex proteins. There aredevices that deposit densely packed arrays of biological materials onmicroscope slides in accordance with these techniques. Aspects of theseand other spot arrayers are described in U.S. Pat. Nos. 6,040,193 and6,136,269, in U.S. Pat. No. 6,955,788, and in International PatentApplication No. PCT/US99/00730 (International Publication Number WO99/36760), all of which are hereby incorporated by reference in theirentireties for all purposes. Other techniques for generating spottedarrays also exist. For example, U.S. Pat. No. 6,040,193 to Winkler, etal., is directed to processes for dispensing drops to generate spottedarrays. The '193 patent, and U.S. Pat. No. 5,885,837 to Winkler, alsodescribe the use of micro-channels or micro-grooves on a substrate, oron a block placed on a substrate, to synthesize arrays of biologicalmaterials. These patents further describe separating reactive regions ofa substrate from each other by inert regions and spotting on thereactive regions. The '193 and '837 patents are hereby incorporated byreference in their entireties. Another technique is based on ejectingjets of biological material to form a spotted array. Otherimplementations of the jetting technique may use devices such assyringes or piezo electric pumps to propel the biological material.Various other techniques exist for synthesizing, depositing, orpositioning biological material onto or within a substrate.

To ensure proper interpretation of the term “probe” as used herein, itis noted that contradictory conventions exist in the relevantliterature. The word “probe” is used in some contexts to refer not tothe biological material that is synthesized on a substrate or depositedon a slide, as described above, but to what has been referred to hereinas the “target.” To avoid confusion, the term “probe” is used herein torefer to probes such as those synthesized according to the VLSPSTMtechnology and other synthesis techniques known in the art; thebiological materials deposited so as to create spotted arrays; andmaterials synthesized, deposited, or positioned on a substrate to formarrays according to other current or future technologies. Thus,microarrays formed in accordance with any of these technologies may bereferred to generally and collectively hereafter for convenience as“probe arrays.” Moreover, the term “probe” is not limited to probesimmobilized in array format. Rather, the functions and methods describedherein may also be employed with respect to other parallel assaydevices. For example, these functions and methods may be applied withrespect to probe-set identifiers that identify probes immobilized on orin beads, optical fibers, or other substrates or media.

Probes typically are able to detect the expression of correspondinggenes or EST's by detecting the presence or abundance of mRNAtranscripts present in the target. This detection may, in turn, beaccomplished by detecting labeled cRNA that is derived from cDNA derivedfrom the mRNA in the target. In general, a group of probes, sometimesreferred to as a probe set, contains sub-sequences in unique regions ofthe transcripts and does not correspond to a full gene sequence. Furtherdetails regarding the design and use of probes are provided in U.S. Pat.No. 6,188,783, in International Patent Application Ser. No.PCT/US01/02316, filed Jan. 24, 2001, and in U.S. patent application Ser.Nos. 09/721,042 (abandoned), 09/718,295 (abandoned), and 09/764,324(abandoned), and U.S. Pat. No. 7,117,095, all of which patents andpatent applications are hereby incorporated herein by reference in theirentireties for all purposes.

Labeled targets in hybridized probe arrays may be detected using variouscommercial devices, sometimes referred to as scanners. Scanners imagethe targets by detecting fluorescent or other emissions from the labels,or by detecting transmitted, reflected, or scattered radiation. Atypical scheme employs optical and other elements to provide excitationlight and to selectively collect the emissions. Also generally includedare various light-detector systems employing photodiodes, charge-coupleddevices, photomultiplier tubes, or similar devices to register thecollected emissions. For example, a scanning system for use with afluorescent label is described in U.S. Pat. No. 5,143,854, incorporatedby reference above. Other scanners or scanning systems are described inU.S. Pat. Nos. 5,578,832, 5,631,734, 5,834,758, 5,936,324, 5,981,956,6,025,601, 6,141,096, 6,185,030, 6,490,533, 6,650,411, 6,643,015 and6,201,639, in International Patent Application PCT/US99/06097 (publishedas WO99/47964), in U.S. patent application Ser. Nos. 09/682,837(abandoned), and in U.S. Provisional Patent Application Ser. Nos.60/364,731 (expired), 60/396,457 (expired), and 60/435,178 (expired),each of which patent and patent application is hereby incorporated byreference in its entirety for all purposes.

It is further contemplated that assays of the present invention willutilize, in some embodiments, “liquid arrays.” As used herein, a liquidarray typically consists of a plurality of encoded microparticles whereeach microparticle has been encoded with one or more features comprisinga distinguishable, pre-determined code. One or more probes can beimmobilized on the surface of each microparticle, often with probesimmobilized on a single particle at densities of, for example, 10⁴/um²or higher. Incorporation of distinguishable, pre-determined codes allowsfor each desired species of probe to be immobilized upon microparticlesof a single distinct code. Assays will then typically hybridize theprobes immobilized on a microparticle with one or more targets from oneor more samples. Labeling methods known in the art can be used withrespect to the samples, microparticles, or both depending on the designof a particular assay. Subsequent detection and quantification of thevarious targets is performed by detection and reading of the codes onthe microparticles and detection and quantification of the desired labelto provide both detection and quantification of the targets. Furtherdetails regarding the design and use of liquid arrays are provided inU.S. Pat. Nos. 7,745,091; 7,745,092; U.S. Published Patent ApplicationNos. 2009/0149340; 2010/0227770; 2010/0227279; 2010/0290018;2010/0297336; 2010/0297448; and U.S. patent application Ser. Nos.60/716,694; 60/762,238; 60/946,127; and 11/521,115, each of which arehereby incorporated herein by reference in their entireties for allpurposes.

IV. Specific Embodiments

Various embodiments are contemplated herein relating to assays thatcapture recognition sites for DNA or RNA binding proteins, convert therecognition sites into double-stranded form if necessary, bind DNA orRNA binding proteins to the recognition sites, and measure the resultingbinding affinities of the selected binding proteins for the particularrecognition sequences of the recognition sites.

Aspects of certain embodiments of the assay are illustrated by FIGS.1(A)-1(C). In FIG. 1(A), a capture oligonucleotide 120 is attached to asubstrate 110. Capture oligonucleotide 120 may be a sequence of DNA orRNA, isolated from natural sources, recombinantly produced orartificially synthesized, and can include modified artificial analogsthereof, such as locked nucleic acids or peptide nucleic acids. Thesequence length of capture oligonucleotide 120 will vary depending onthe particular embodiment, but will generally be at least 10 nucleotidesin length, and may be significantly longer in length, such as lengths of100 nucleotides. Sequence lengths within these two values are alsopossible, for example, lengths of 10, 11, 12, 13, 14, 15, 20, 25, 30,35, 40, 50, 60, 75, or 90 nucleotides. Other embodiments may utilizesequence lengths for capture oligonucleotide outside of this range, suchas 8, 9, 105 or 110 nucleotides. Capture oligonucleotide 120 may beattached to substrate 110 at its 5′ or 3′ end. It should be furthernoted that substrate 110 can be any suitable substrate as discussedherein, and configured for a variety of array formats, including, forexample, Affymetrix GENECHIP® arrays, other high density microarrayformats, spotted arrays, liquid arrays, inkjet arrays, bead arrays andother array formats compatible with the various embodiments disclosedherein. Capture oligonucleotide 120 may be attached to substrate 110through in situ synthesis via, for example, a photolithographic approachutilizing photodeprotection with masks, photolithography utilizingdigital micromirrors, or an inkjet printing approach utilizing chemicaldeprotection. Capture oligonucleotide 120 may also be attached tosubstrate 110 after capture oligonucleotide 120 has been synthesized,such as by covalent attachment via an aliphatic amine group at the 5′end of capture oligonucleotide 120. Additionally, captureoligonucleotide 120 may be directly attached to substrate 110, orthrough other means known in the art, such as through a linker molecule,for example lysine, epoxy-silanes (e.g., 3-glycidoxypropyltrimethoxysilane), or amino-silanes (e.g., 3-aminopropyltrimethoyxsilane), or many other alternatives known in the art.Furthermore, each substrate 110 may have a single captureoligonucleotide 120, multiple copies of a particular captureoligonucleotide 120, single copies of a plurality of different captureoligonucleotides 120, or multiple copies of a plurality of differentcapture oligonucleotides 120. Capture oligonucleotides 120 may beattached in any suitable arrangement and density, such as in apre-determined grid, a random attachment with subsequent identificationof the location of each capture oligonucleotide 120, or through othermeans known in the art. Substrate 110 may include additional componentsdepending upon the embodiment. For example, embodiments utilizing liquidarrays comprise a plurality of microparticles, where each microparticlehas been encoded with one or more features comprising a distinguishable,pre-determined code. Subsequent detection of the code, in correlationwith the capture oligonucleotides 120 attached to the microparticlesubstrate, facilitates the measurement of binding affinities of variousbinding proteins for one or more recognition sites. Other embodiments,for example, may attach one or more capture oligonucleotide 120 s toother substrates, such as beads, where the substrate is individuallydistinguishable from other substrates within the assay that possessdifferent capture oligonucleotides. Such beads have been commercializedwithin, for instance, the xMAP® technology for multiplexing utilizingcolor-coded microspheres (Luminex Corporation, Austin, Tex.). It shouldbe noted, however, that not all embodiments will attach captureoligonucleotides 120 to a substrate. Alternative embodiments maymaintain capture oligonucleotides 120, for example, in-solution.

Capture oligonucleotide 120 includes a complementary region (orcomplementary portion, as used interchangeably herein) that iscomplementary to at least a portion of target fragment 130, and whichwill hybridize with target fragment 130, as illustrated in FIG. 1(A).Furthermore, in certain embodiments, the complementary portion ofcapture oligonucleotide 120 is a unique sequence. The uniqueness may bewith respect to, for example, the overall genome of the sample at issue,or merely the prepared and processed sample (e.g., after selectiveamplification or other complexity reduction methods). The complementaryportion is also a unique, conserved sequence in some embodiments. Thedistance between the complementary portion of capture oligonucleotide120 and recognition site 150 will vary depending upon the embodiment. Insome embodiments there will be no intervening nucleotides between thecomplementary portion of capture oligonucleotide 120 and the firstnucleotide of the recognition sequence of recognition site 150. In otherembodiments, there may be a number of intervening nucleotides, forexample, between 1 and 100 nucleotides, such as 1, 5, 10, 15, 20, 30,40, 50, 75, 100, 150, 200 or more nucleotides. The number of interveningnucleotides may also fall within this range. Embodiments which mayutilize a number of intervening nucleotides include, for example,embodiments where it is desired for the complementary portion of captureoligonucleotide 120 to be a unique sequence, or a unique conservedsequence, which depending on the distance to the nearby recognition siteof interest, may require a number of intervening nucleotides.

In some embodiments, the complementary portion of captureoligonucleotide 120 may consist of the entirety of captureoligonucleotide 120, while in other embodiments only a segment ofcapture oligonucleotide 120 is complementary to target fragment 130.FIGS. 1(A)-1(C) depict embodiments where there is at least onenucleotide of capture oligonucleotide 120 that is not complementary totarget nucleic acid fragment 130. Furthermore, the length of thecomplementary portion will vary depending on the embodiment and desiredcharacteristics of the array. For example, if higher specificity withrespect to target nucleic acid fragment 130 is desired, thecomplementary portion may be, for example, 25, 30, 35, 40, 45, 50, 60 or70 nucleotides in length (as well as nucleotide lengths within thisrange and longer nucleotide lengths). If the desired array is to containa larger number of capture oligonucleotides 120 for a lower relativecost, then the complementary portion may be smaller in length, forexample 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,24, or 25. Additionally, the length of the complementary portion, andthe length of capture oligonucleotide 120 in general, will depend onother factors, such as the desired method of producing captureoligonucleotide 120. The length of the complementary portion willdirectly affect the required length of capture oligonucleotide 120. Forinstance, if a complementary portion length of 25 nucleotides isdesired, then capture oligonucleotide 120 must be at least 25nucleotides in length. In some embodiments, capture oligonucleotide 120includes additional portions. These additional portions may providesupplemental functionality, such as a specific address portion to enableprecise identification of capture oligonucleotide 120. Thus, in someembodiments, in addition to the complementary portion, captureoligonucleotide 120 may include a unique sequence of nucleotides to aidin the exact identification of capture oligonucleotide 120 relative toother capture oligonucleotides 120 that may be utilized within the sameassay or upon the same substrate. In such embodiments, the minimumlength of capture oligonucleotide 120 will be dependent upon, forexample, both the length of the complementary portion and also thelength of the identification sequence. For example, if length of thecomplementary portion is 50 nucleotides and the length of theidentification portion is 29 nucleotides, then capture oligonucleotide120 will be at least 79 nucleotides in length.

Target fragment 130 is a nucleic acid sequence. Target fragment 130 maybe from any sample of interest, taken from any particular organism ofinterest, eukaryotic or prokaryotic. Non-limiting examples include,e.g., human, chimpanzee, dog, rat, Saccharomyces cerevisiae, orEscherichia coli samples. In other embodiments, target fragment 130 isnot from a sample taken from an organism, but is the result ofrecombinant synthesis, artificial synthesis, etc. For example, mutationswithin a recognition sequence can significantly affect the bindingaffinity of a binding protein for that recognition sequence, and someembodiments may utilize one or more synthesized mutant target fragments130 with one or more mutations, such as SNPs, insertions, deletions orinversions, within the recognition sequence of recognition site 150.Accordingly, certain embodiments may use a plurality of differing targetfragments 130 within a single assay, with the number depending uponfactors such as the type and number of substrate employed, desired arraycharacteristics, and the number of binding proteins and recognitionsites of interest. Thus, embodiments may include libraries of varioustarget fragments 130 with a plurality of mutations introduced such thata plurality of recognition site 150 variants are assayed for theirbinding affinity with the binding proteins of interest.

Target fragment 130 may be processed and prepared for the assay throughany suitable means known in the art. For example, a sample may be takenfrom an individual organism, and then amplified by polymerase chainreaction, ligase chain reaction, transcription-based amplification,modifications thereof, and other techniques. For instance, a genomic DNAsample may be digested with restriction enzymes, such as Nsp I and StyI, before adaptor ligation to the resulting fragments, PCR amplificationof the adaptor-ligated fragments, and subsequent fragmentation (e.g.,through restriction enzymes or acoustical shearing) of the amplifiedDNA. In some embodiments, target fragment 130 may be introduced tosubstrate 110 with an adaptor sequence added to one or both ends.Various techniques known in the art can be utilized to improve thequality of target fragments 130. For example, amplification of thetarget sample is useful in minimizing the influence of methylated DNA,where methylation may partially obstruct binding proteins fromsuccessfully binding to a recognition site. Methylation may also causethe target fragment 130 to already be bound by other binding proteins,such as methyl-CpG-binding domain proteins, which bind to methylatedgene promoters. However, it should be noted that in some embodiments,maintaining the methylation that may be present in the original samplemay be desirable. In such circumstances, various techniques may be usedto prevent demethylation, such as the inclusion of DNA methyltransferase1, during amplification of the sample.

FIG. 1(B) illustrates the next step in certain embodiments of the assay.Here, at least a portion of target fragment 130 that remainssingle-stranded is made double-stranded by the synthesis ofcomplementary fragment 140. The resulting double-stranded portion willdesirably include at least a binding protein recognition site 150. Thelength and exact nucleotides of the recognition sequence of recognitionsite 150 will depend upon the binding protein and recognition site ofinterest. For example, SP1 has a recognition sequence 6 nucleotides inlength, Oct-1 has a recognition sequence 8 nucleotides in length, andNF-1 has a recognition sequence 15 nucleotides in length. The synthesisof the complementary fragment 140 can be accomplished by various meansknown in the art. For example, in embodiments such as those illustratedby FIG. 1(A)-1(C), where capture oligonucleotide 120 is attached at its5′ end to substrate 110, a DNA polymerase, such as the exo-Klenowfragment of DNA polymerase I, can be utilized to extend captureoligonucleotide 120 by creating complementary fragment 140 byincorporation of appropriate dNTPs, thus making target fragment 130 andrecognition site 150 double-stranded. Various means, such as a DNAligase (e.g., Taq DNA Ligase), are used in certain embodiments to createa phosphodiester bond between the 3′ hydroxyl termini and 5′ phosphatetermini of capture oligonucleotide 120 and complementary fragment 140.For other embodiments, such as those where capture oligonucleotide 120is attached at its 3′ end to substrate 110, complementary fragment 140would be synthesized by other methods known in the art. For example, DNAprimase, DNA polymerase δ, DNA ligase I, flap endonuclease 1, and Dna2endonuclease can be utilized to create complementary fragment 140 whencapture oligonucleotide 120 is attached at its 3′ end. Embodimentsutilizing this step of the assay to produce double-stranded nucleicacids may additionally include a step to remove extraneoussingle-stranded nucleic acids. This can be performed by various means inthe art, such as utilizing exonuclease Ito digest unbound fragments ofnucleic acids from the sample and unbound capture oligonucleotides 120through its 3′ to 5′ single-strand digestion in embodiments wherecapture oligonucleotides 120 are attached to substrate 110 at their 5′end. Other embodiments may utilize one or more washing steps aftersynthesis of complementary fragment 140 to remove unbound fragments ofnucleic acids from the sample, in addition to other purposes, such asremoving a target fragment 130 which did not completely hybridize withthe complementary portion of capture oligonucleotide 120 because ofsequence differences.

Additional embodiments may omit the step of synthesizing complementaryfragment 140, and additional steps, such as the digestion ofsingle-stranded nucleic acids, if the binding proteins of interest bindto single-stranded nucleic acids, such as Replication protein A, whichbinds to single-stranded DNA, or Polyadenylate-binding protein 1, whichbinds to mRNA. Other embodiments directed to binding proteins specificfor single-stranded nucleic acids will still utilize the step ofsynthesizing complementary fragment 140. In these embodiments, targetfragment 130 will be used to guide the proper synthesis of complementaryfragment 140, wherein for these embodiments the desired recognitionsequence of recognition site 150 is located within complementaryfragment 140. After synthesis of complementary fragment 140 is complete,the resulting double-stranded oligonucleotide is separated so thattarget fragment 130 can be removed, thus making recognition site 150 oncomplementary fragment 140 available for subsequent binding by a bindingprotein 160. Separation of the double-stranded oligonucleotides can beaccomplished by a variety of means known in the art, such as throughthermal denaturation, or enzymatically through the use of, for example,a helicase.

Creation of complementary fragment 140 based upon the exact sequence oftarget fragment 130 provides important advantages to alternative methodsof forming an array for the measurement of binding protein affinities,such as manufacturing arrays of double-stranded oligonucleotides anddirectly adding the binding proteins of interest. While target nucleicacid fragment 130 may be obtained from any desired source, includingartificial synthesis, it is desirable in many embodiments to obtain thegenomic sample to be assayed from the individual organism of interest,for instance, a human patient or a laboratory animal. Use of aparticular individual organism to supply target fragments 130 allowscreation of recognition sites 150 that are specific to the individualwhich supplied the sample. Thus, mutations within the sequence ofrecognition site 150, such as SNPs, insertions, deletions or inversions,which are present within the organism, will also be present withinrecognition site 150. Furthermore, this customization of the recognitionsites 150 to be assayed with the binding proteins of interest does notrequire the creation of a custom array for each individual because it isnot necessary to customize substrate 110 and capture oligonucleotides120. Thus, capture oligonucleotides 120 may remain the same between twoarrays of a particular assay type, even when two distinct individualsare being assayed, which simplifies manufacturing and lowers costs whilestill providing an assay that is customized to the particular individualof interest. This advantage is also present within embodiments directedto assaying binding affinities of single-stranded binding proteins andwhich do not utilize the creation of complementary fragment 140, astarget fragment 130, which contains recognition site 150 in thoseembodiments, is still specific to the individual of interest in thoseembodiments. Additionally, the assay is not limited to recognition sites150 of a particular size, as would be a case with a protein bindingmicroarrays that contains, for example, all sequence variants of aparticular size, such as 8mers or 10mers. For example, Nuclear factor Ibinds to a recognition sequence that is 15 nucleotides in length, andtherefore such binding proteins could not be assayed with such a proteinbinding microarray.

FIG. 1(C) illustrates the subsequent step in certain embodiments of theassay. At least one binding protein 160 is introduced to substrate 110and allowed to potentially bind to recognition site 150. The type andsource of nucleic acid binding protein 160 will vary depending on theassay being performed. Embodiments focusing on common binding proteinscan utilize commercially obtained binding proteins, such as the TATA-boxbinding protein (TBP) or p53 protein, available from, for example, JenaBioscience GmbH (Jena, Germany). In some circumstances, binding proteinswith mutations, such p53 proteins with specific mutations, may also beavailable commercially and be utilized to determine the differences inbinding affinity of a mutant protein for a particular recognition sitein relation to the wild type binding protein. However, obtaining bindingproteins with all of the mutations desired for a particular assay maynot always be possible or feasible. Furthermore, embodiments of theassay utilizing binding proteins specific to the particular individualorganism of interest can provide a significant advantage in determiningmore accurate binding affinities, especially when these embodimentsutilize target fragments 130 that are also specific to the individual. Acombination of binding proteins 160 and target fragments 130 that arespecific to the individual creates an assay that is entirely specific tothe individual while being of a common design, with the one or moresubstrates 110 with the common and pre-designed capture oligonucleotides120. Binding proteins specific to an individual can be acquired throughvarious means known in the art, such as through in vitro translation ofrecombinant proteins utilizing plasmid DNA or PCR products with lysatesof required translational machinery components from, for example,Escherichia coli. Other methods known in the art can also be utilizedfor production of desired binding proteins, for example, in vivoexpression techniques that may, for instance, transform cells withplasmid DNA, cultivating and lysing transformed cells, and purifying thedesired proteins. Translation of proteins through in vitro techniques ispossible with commercially available kits, such as the EasyXpressProtein Synthesis Kit (Qiagen, Inc., Valencia, Calif.). Such techniquesfacilitate the production in vitro of, for example, a particularpatient's binding proteins, with any mutations that may be present, forfurther analysis within the assay. This allows not only forcustomization of the binding proteins within the assay to an individual,but also the use of mutant variants of binding proteins that are rare orpreviously unknown, and that would otherwise not be available. Suchembodiments of the assay utilizing recognition sites 150 and bindingproteins 160 that are specific to the individual of interest allowmeasurement of the binding affinities of interest on a level that ismore specific than other available assays, and can allow the detectionof genetic disorders and the diagnosis of medical conditions whenknowledge of the mutation within the recognition site and/or the bindingprotein alone is insufficient. Assays that are personalized with respectto only the recognition sites or the binding proteins of interest willnot always detect and/or properly measure changes in binding affinity,especially in situations where both the recognition sequence at issueand the binding domain of the protein at issue both contain one or moremutations.

Recombinant protein production also provides the ability to use aplurality of mutant forms of a particular binding protein withinembodiments of the assay. Embodiments may utilize this ability invarious ways, such as the creation of multiple mutant variants of abinding protein to compare their associated binding affinities with oneor more recognition sites. Creation of mutant forms of binding proteinsis also useful for a variety of research purposes, such as, for example,the creation of modified artificial transcription factors in therapeuticgene modulation research that seeks to alter the expression of aparticular gene or pathway. Embodiments of the assay utilize multiplemutant forms of a binding protein to measure their relative bindingaffinities with one or more recognition sites 150, with one or morepossible recognition sequences for each recognition site. Such assayscan be particularly useful, for example, in measuring the differences inthe binding affinity of various mutant versions of a binding proteinthat are present in a population for the various mutant versions of itscorresponding recognition site that are also present in the population,and allowing such measurements without having to find individualspossessing all of the mutant versions.

FIG. 1(C) illustrates an embodiment where binding protein 160 comprisesa label 170. Label 170 may be any suitable label known in the art. Label170 may be, for example, a fluorescent label, such as an organic dye(e.g., fluorescein, Cy3, Cy5, rhoadamine), a biological fluorophore(e.g., phycoerythrocyanin), or a quantum dot (e.g., a carboxyl quantumdot). Fluorescent labels may include, for example, N-hydroxysuccinimideester activated dyes that react with exposed amino groups, malemideactivated dyes that react with sulfhydryl groups, phosphine activateddyes that react with azide groups, or other suitable labels known in theart. Depending on the embodiment, suitable labels may be availablecommercially from, for example, Invitrogen (Carlsbad, Calif.), ThermoFisher Scientific (Waltham, Mass.), and ATTO-TEC GmbH (Siegen, Germany).Depending on the embodiment, a variety of fluorescent labels withdifferent excitation and emission characteristics can be utilized withthe various binding proteins 160 of the assay. For example, an exemplaryassay may have one or more types of binding proteins labeled withdifferent fluorescent labels, each producing different emission colors,such as non-limiting examples of blue, green, yellow, orange and red(and/or multiple shades of one or more of these colors and theirrespective emission spectra). Furthermore, in some embodiments, abinding protein 160 may have a combination of dyes to produce a distinctfluorescent profile for a particular binding protein 160 within theassay. Depending on the number and variety of binding proteins 160, thenumber and variety of recognition sites 150 and their bindingsuitability with respect to the binding proteins 160 that will bepresent, the preferred label or labels to be utilized, and other assaycharacteristics of the particular embodiment, labeling may be performedbefore binding proteins 160 are introduced within the assay, duringbinding, or subsequent to binding. The labeling of binding proteins 160may occur in a single step, or within multiple steps (e.g., singlelabeling step of labeled antibodies appropriate for the binding proteinsat issue, sandwich labeling with labeling molecular pairs such as biotinand streptavidin, etc.). Embodiments may utilize various proceduresknown in the art to optimize detection and proper measurement of boundbinding proteins and their associated labels, such as washing to removeunbound binding proteins. As well, some embodiments may use additionalfluorescent labels within the assay for the purposes of, for example,imaging calibration, background controls, normalization, or minimizingthe effects of hybridization variation. These additional labels may beincorporated within the assay through, for example, captureoligonucleotide 120, target fragment 130, complementary fragment 140, orbinding protein 160. Detection of fluorescent labels may be accomplishedin embodiments of the assay through a variety of methods utilizingsuitable instruments known in the art. These include, for example,scanning methods and systems as described in U.S. Pat. Nos. 5,143,854;5,578,832; 5,631,734; 5,834,758; 5,936,324; 5,981,956; 6,025,601;6,141,096; 6,185,030; 6,201,639; 6,490,533; 6,643,015; 6,650,411;6,741,344; 6,813,567; 7,095,032; 7,062,092; 7,148,492; 7,222,025;7,312,919; 7,317,415; 7,406,391; 7,682,782; and 7,689,022; each of whichis hereby incorporated by reference in its entirety for all purposes.

Detection of the resulting intensity level of a fluorescent labelprovides, at least in part, a measurement of the affinity between theone or more binding proteins 160 labeled with that particular label 170for the one or more recognition sites 150 created through thecorresponding capture oligonucleotides 120, target fragments 130 andcomplementary fragments 140. Both absolute and relative quantificationof labeling, fluorescent or otherwise (e.g., ³²P or ¹²⁵I labeling), iswell known in the art. See, e.g., Yan and Marriott, “Analysis of proteininteractions using fluorescence technologies,” Current Opinion inChemical Biology, 7: 635-640 (2003); Haab et al., “Protein microarraysfor highly parallel detection and quantitation of specific proteins andantibodies in complex solutions,” Genome Biology, 2(2):research0004.1-0004.13 (2001); and Ge, “UPA, a universal protein arraysystem for quantitative detection of protein-protein, protein-DNA,protein-RNA and protein-ligand interactions,” Nucleic Acids Research,28(2): e3, i-vii (2000). Relative quantifications can be especiallyuseful within embodiments utilizing two or more variants of a bindingprotein, or related binding proteins, such as a wild type variant of abinding protein and one or more mutant variants of the same protein. Insuch embodiments, each variant could possess, for instance, adistinguishable label in order to construct a comparison of the relativebinding affinities of each binding protein variant for a particularrecognition site 150 by measuring and comparing the signal intensitiesfor each variant (e.g., comparing signal intensity ratios for onebinding protein variant relative to another binding protein variant).

Additional processing, such as normalization of signal intensities andbackground calibration, can further refine the measured signalintensities into measurements of binding affinity. Further refinementmay be possible by other techniques, such as incorporation of particularfluorescent label(s) into capture oligonucleotides 120, target fragments130, complementary fragments 140, and/or binding proteins 160 for thepurposes of normalization, background, use as controls, or other use ofthe resulting intensity values in order to account for variations withinthe assay of the one or more labels 170. For example, depending on theassay design, the various target fragments 130 may have slightlydifferent hybridization kinetics with respect to their correspondingcapture oligonucleotides 120. Accordingly, different features of anarray may have slight relative differences in the quantities of targetfragments 130 bound to their respective capture oligonucleotides 120.These differences can then affect the resulting signals from labels 170associated with binding proteins 160. Therefore, normalization and othertechniques to even out or otherwise account for these differences canpositively influence the eventual data utilized in assessing therelevant binding protein affinities.

Other suitable methods of labeling, either directly or indirectly, arealso possible according to embodiments of the assay. For example, label170 may also be an antibody, with an associated label or tag to beutilized with the antibody to enable detection, such as a radioisotope,enzymatic tag (e.g., horseradish peroxidase), or a fluorescent tag(e.g., utilizing a biotin labeled antibody with subsequent use ofstreptavidin). While antibodies are not required for labeling anddetection of binding protein 160, they may be convenient depending onthe binding proteins of interest and availability of suitableantibodies. For example, if a common binding protein is of interest,labeled specific antibodies for that protein may be readily available.Other known labeling features are also possible in various embodiments,such as the use of a fluorescent dye in combination with a labeledantibody (e.g., labeling a protein with sulforhodamine 101 acid chlorideand utilizing labeled antibodies which recognize that fluorophore).Regardless of the manner of labeling employed, however, an importantfeature of the various embodiments is that the entire assay can bepersonalized to an individual of interest while also allowing the assayto be performed entirely in vitro. This allows in vivo steps to beomitted, and that are otherwise required in other techniques, such asthose involving chromatin immunoprecipitation.

While FIGS. 1(A)-1(C) depict a single capture oligonucleotide 120attached to a single substrate 110, and the use of a single bindingprotein 160, it should be appreciated that each of these elements willbe present in multiplicative form in various embodiments. For example,while some embodiments may utilize a single substrate 110 whichpossesses one or more capture oligonucleotides 120, other assayembodiments utilize multiple substrates 110. For example, embodimentsmay use beads, microspheres or microparticles as substrate 110, andwhich may number, for example, from a single substrate to thousands ormillions depending on the particular design of the assay. Each substrate110 may possess a single capture oligonucleotide 120, multiple copies ofa single capture oligonucleotide 120, one copy each of a plurality ofcapture oligonucleotides 120, or multiple copies of multiple differentcapture oligonucleotides 120. In this manner, embodiments of the assayare able to capture one or more target fragments 130 with one or moresubstrates 110. For instance, a substrate 110, or a combination ofsubstrates 110, may possess twenty copies of the a particular captureoligonucleotide 120, such that up to twenty target fragments 130 allcontaining the same recognition site 150 are captured onto substrate110. Subsequently, one or more of the corresponding binding protein 160variants (e.g., the wild type binding protein and one or more mutantversions of the binding protein, or a selection of wild and mutantvariants from within a family of binding proteins) are introduced tosubstrate 110. Detection of the one or more types of utilized labels 170can then provide information regarding the binding affinities of thedifferent variants of the binding protein 160 with respect torecognition site 150. Embodiments of the assay further envisioncombining this binding affinity information with information about theprecise sequence of the one or more recognition sites 150, obtained byvarious means known in the art, such as, for example, sequencing byhybridization, chain-termination sequencing, dye-terminator sequencing,massively parallel signature sequencing, Polony sequencing,pyrosequencing, reversible dye-terminator sequencing, sequencing byligation, ion semiconductor sequencing, or unchained sequencing byligation of nucleic acid nanoballs. Combining the obtained informationfacilitates the analysis of the binding affinity of multiple differentbinding proteins (and mutant variants thereof) with the exactrecognition sequences of the relevant recognition sites, with all thedata entirely personalized to the individual of interest. This can beparticularly advantageous when an individual is suffering from acondition or disease that may result from one or more mutations withinthe recognition sequence of a recognition site 150, and which alsoresults from one or more mutations within the binding protein 160 whichaffect the protein's binding ability with its normal correspondingrecognition sequence.

Furthermore, while FIGS. 1(A)-1(C) depict a single binding protein 160involved with recognition site 150, some embodiments of the assay aredirected to the measurement of binding affinities of binding proteinswhich operate in association with other cellular molecules, such asregulatory proteins, transcription cofactors or miRNAs. For example, thetranscription factor Mcml interacts with, depending on the cell type andgenes at issue, the cofactors α1, α2, and Ste12. Mcml forms a complexwith α1 alone, with both α1 and α2 simultaneously, or with Stel2 alonedepending on the cell type and genes at issue. Thus, embodiments of theassay will utilize a particular binding protein 160 with one or moreassociated molecules affecting its binding activity, such astranscription cofactors or miRNAs. Such embodiments facilitate thecomparative measurement of the affinity of a binding protein 160 for oneor more recognition sites 150 when the assay is performed with one ormore cofactors to enable, for example, the measurement of the bindingaffinity when the binding protein 160 is complexed with one cofactor incomparison to being complexed with another cofactor. Furthermore,certain embodiments will introduce one or more mutations within bindingprotein 160 or these associated proteins so that the binding affinity ofthe resulting complex or otherwise altered binding protein 160 can beaccurately measured with respect to the recognition site 150 at issue.As with binding protein 160, these other proteins may be specific to theindividual of interest and are acquired through suitable in vitro or invivo techniques to preserve any possibly relevant mutations so that theeffect of the mutations will be incorporated within the assay.Additionally, embodiments incorporating molecules associated withbinding protein 160 and which may subsequently affect the bindingaffinity for recognition site 150 may further include one or more labels170 associated with one or more components of the combined bindingcomplex. For example, a binding protein 160 and a cofactor protein maybe labeled in a florescence resonance energy transfer (FRET) manner,where, for instance, either the binding protein 160 or the cofactorprotein is labeled with a donor dye and the other molecule is labeledwith the acceptor dye. Subsequent binding of the binding protein 160 andthe cofactor protein, and detection of the acceptor emission upon donorexcitation, allows detection of the protein complex. Non-limitingexamples of FRET pairs are Cy2-Cy3 or Cy3-Cy5. Some embodiments mayincorporate fluorescent proteins into proteins utilized within theassay, for example variants of green fluorescent protein such as cyanfluorescent protein utilized with yellow fluorescent protein.

Additional aspects of certain embodiments of the assay are illustratedby FIGS. 2(A)-2(C). These embodiments utilize an approach partiallybased upon molecular inversion probe (MIP) technology. Various aspectsof MIP technology are described in, for example, Hardenbol et al.,“Multiplexed genotyping with sequence-tagged molecular inversionprobes,” Nature Biotechnology, 21(6): 673-678 (2003); Hardenbol et al.,“Highly multiplexed molecular inversion probe genotyping: Over 10,000targeted SNPs genotyped in a single tube assay,” Genome Research, 15:269-275 (2005); Burmester et al., “DMET microarray technology forpharmacogenomics-based personalized medicine,” Methods in MolecularBiology, 632: 99-124 (2010); Sissung et al., “Clinical pharmacology andpharmacogenetics in a genomics era: the DMET platform,”Pharmacogenomics, 11(1): 89-103 (2010); Deeken, “The Affymetrix DMETplatform and pharmacogenetics in drug development,” Current Opinion inMolecular Therapeutics, 11(3): 260-268 (2009); Wang et al., “Highquality copy number and genotype data from FFPE samples using MolecularInversion Probe (MIP) microarrays,” BMC Medical Genomics, 2:8 (2009);Wang et al., “Analysis of molecular inversion probe performance forallele copy number determination,” Genome Biology, 8(11): R246 (2007);Ji et al., “Molecular inversion probe analysis of gene copy alternationsreveals distinct categories of colorectal carcinoma,” Cancer Research,66(16): 7910-7919 (2006); and Wang et al., “Allele quantification usingmolecular inversion probes (MIP),” Nucleic Acids Research, 33(21): e183(2005), each of which is hereby incorporated by reference in itsentirety for all purposes. See also in U.S. Pat. Nos. 6,858,412;5,817,921; 6,558,928; 7,320,860; 7,351,528; 5,866,337; 6,027,889 and6,852,487, each of which is hereby incorporated by reference in itsentirety for all purposes.

MIP technology has previously been successfully applied to other areasof research, including the novel identification and subclassification ofbiomarkers in cancers. See, e.g., Brewster et al., “Copy numberimbalances between screen- and symptom-detected breast cancers andimpact on disease-free survival,” Cancer Prevention Research, 4(10):1609-1616 (2011); Geiersbach et al., “Unknown partner for USP6 andunusual SS18 rearrangement detected by fluorescence in situhybridization in a solid aneurysmal bone cyst,” Cancer Genetics, 204(4):195-202 (2011); Schiffman et al., “Oncogenic BRAF mutation with CDKN2Ainactivation is characteristic of a subset of pediatric malignantastrocytomas,” Cancer Research, 70(2): 512-519 (2010); Schiffman et al.,“Molecular inversion probes reveal patterns of 9p21 deletion and copynumber aberrations in childhood leukemia,” Cancer Genetics andCytogenetics, 193(1): 9-18 (2009); Press et al., “Ovarian carcinomaswith genetic and epigenetic BRCA1 loss have distinct molecularabnormalities,” BMC Cancer, 8:17 (2008); and Deeken et al., “Apharmacogenetic study of docetaxel and thalidomide in patients withcastration-resistant prostate cancer using the DMET genotypingplatform,” Pharmacogenomics, 10(3): 191-199 (2009), ach of which ishereby incorporated by reference in its entirety for all purposes.

MIP technology has also been applied to the identification of newdrug-related biomarkers. See, e.g., Caldwell et al., “CYP4F2 geneticvariant alters required warfarin dose,” Blood, 111(8): 4106-4112 (2008);and McDonald et al., “CYP4F2 Is a Vitamin K1 Oxidase: An Explanation forAltered Warfarin Dose in Carriers of the V433M Variant,” MolecularPharmacology, 75: 1337-1346 (2009), each of which is hereby incorporatedby reference in its entirety for all purposes. Other MIP applicationsinclude drug development and safety research. See, e.g., Mega et al.,“Cytochrome P-450 Polymorphisms and Response to Clopidogrel,” NewEngland Journal of Medicine, 360(4): 354-362 (2009); Dumaual et al.,“Comprehensive assessment of metabolic enzyme and transporter genesusing the Affymetrix Targeted Genotyping System,” Pharmacogenomics,8(3): 293-305 (2007); and Daly et al., “Multiplex assay forcomprehensive genotyping of genes involved in drug metabolism,excretion, and transport,” Clinical Chemistry, 53(7): 1222-1230 (2007),each of which is hereby incorporated by reference in its entirety forall purposes. Further applications of MIP technology include genotypeand phenotype databasing. See, e.g., Man et al., “Genetic Variation inMetabolizing Enzyme and Transporter Genes: Comprehensive Assessment in 3Major East Asian Subpopulations With Comparison to Caucasians andAfricans,” Journal of Clinical Pharmacology, 50(8): 929-940 (2010),which is hereby incorporated by reference in its entirety for allpurposes.

FIGS. 2(A)-2(C) illustrate a non-limiting example of certain embodimentsutilizing an approach which utilizes the aspect of two captureoligonucleotides for a single target in combination with a gap fillreaction to complete a double-stranded nucleic acid for further use.Many aspects of the embodiments illustrated by FIGS. 2(A)-2(C), however,will be similar with respect to the embodiments illustrated by FIGS.1(A)-1(C). A second non-limiting example of a different MIP variation isillustrated within FIGS. 4(A)-4(D) and 5(A)-5(C).

In FIG. 2(A), a first capture oligonucleotide 220 and a second captureoligonucleotide 225 are attached to substrate 210. First and secondcapture oligonucleotides 220 and 225 can be attached to substrate 110 attheir 5′ and 3′ ends, respectively, or in the reverse configuration,depending on the particular assay configuration and embodiment. Asdescribed earlier with respect to capture oligonucleotide 120, first andsecond capture oligonucleotides 220 and 225 may be synthesized orattached (after synthesis) to substrate 210 through any suitable methodand may comprise any suitable number of nucleotides. At least a portionof first capture oligonucleotide 220 is complementary to a first regionof target fragment 130, while at least a portion of second captureoligonucleotide 225 is complementary to a second region of targetfragment 230. FIGS. 2(A)-2(C) depict an embodiment where the entirety offirst capture oligonucleotide 220 and second capture oligonucleotide 225is complementary to a first region of target fragment 130 and a secondregion of target fragment 130, respectively. In other embodiments, oneor more nucleotides of first and second capture oligonucleotides 220 and225 may not be complementary to the first and second regions of targetfragment 130, respectively. The one or more non-complementarynucleotides may be, for example, nucleotides utilized as a linker orspacer between substrate 110 and the portions of first and secondcapture oligonucleotides 220 and 225 that are complementary to regionsof target fragment 130. Depending on the embodiment of the assay and thelocation of recognition site 150, one or both of captureoligonucleotides 220 and 225 may be unique sequences. Additionally, insome embodiments, one or both of capture oligonucleotides 220 and 225may be unique, conserved sequences. However, in other embodiments,neither first capture oligonucleotide 220 nor second captureoligonucleotide 225 is a unique or conserved sequence. In a situationwhere neither of the capture oligonucleotides 220 and 225 are unique,capture of the desired target fragment 130 is accomplished by, forexample, selection of the sequences for the first and second captureoligonucleotides such that the combination of the two oligonucleotidesequences and the distance between them is unique for the desiredsample, or at least the desired sample as prepared and processed (e.g.,after selective amplification). In some embodiments, one of captureoligonucleotides 220 and 225 corresponds to an adaptor sequence, whereinthe corresponding complementary adaptor sequence has been added totarget fragment 130. As depicted in FIG. 2(B), first captureoligonucleotide 220 is downstream of the recognition site 150 ofinterest while second capture oligonucleotide 225 is upstream of therecognition site 150 of interest, both with respect to target fragment130, but it should be appreciated that in other embodiments theorientation can be reversed.

FIG. 2(B) illustrates the next step in certain embodiments of the assay,where target fragment 130 is made double-stranded by the synthesis ofcomplementary portion 140. The resulting double-stranded portion willinclude at least recognition site 150. This can be accomplished byvarious means known in the art, such as for example, enzymatically via aDNA polymerase and a DNA ligase, such as the exo-Klenow fragment of DNApolymerase I and Taq DNA ligase. In some embodiments, if a DNApolymerase is utilized, the free 3′ end of first or second captureoligonucleotide 220 or 225 (depending on the respective orientations ofeach with respect to substrate 110) is extended until the 5′ end of theother capture oligonucleotide 220/225 is reached, and an appropriate DNAligase is then utilized to join the strands. Also, as before,embodiments may utilize additional steps, such as removing extraneousnucleic acids with, for example, exonuclease Ito remove single-strandedDNA from the assay. Furthermore, embodiments utilizing first and secondcapture oligonucleotides 220 and 225 may also omit the step ofsynthesizing complementary fragment 140 if the binding proteins 160 ofinterest bind to single-stranded nucleic acids and recognition site 150is located on target fragment 130.

FIG. 2(C) illustrates the subsequent step in certain embodiments of theassay, and is quite similar to the described embodiments associated withFIG. 1(C), as the primary difference in the assay at this step is thatthe double-stranded oligonucleotide containing recognition site 150 inthis embodiment is attached to substrate 110 at both ends while in theembodiments depicted in FIG. 1(C), the oligonucleotide is only attachedto substrate 110 at one end.

Other embodiments utilize other variations of MIP technology approach,such as where a single MIP polynucleotide probe is employed in-solutionto facilitate selective amplification of one or more regions of interestwithin a sample of nucleic acids before those selected regions aresubsequently utilized as target fragments 130 in a binding proteinaffinity assay. Such variations of MIP technology are described within,for example, the earlier referenced patents and non-patent literaturerelating to MIP technology and its applications within the novelidentification and subclassification of biomarkers in cancers, theidentification of new drug-related biomarkers, genotype and phenotypedatabasing, and other applications.

A non-limiting example of such a MIP probe and its structure during theassay is illustrated within FIG. 3. A nucleic acid of interest 305 isthe target for a MIP probe. MIP probe 310 illustrates a non-limitingexample of the initial, starting form of the MIP probe that is added tothe sample containing nucleic acid 305. MIP probe 315 is thecircularized version of MIP probe 310 after hybridization with nucleicacid 305. MIP probe 320 is the subsequent linearized version ofcircularized MIP probe 315.

MIP probe 310 comprises several components, including a first genomichomology region 330 and a second genomic homology region 335. First andsecond genomic homology regions 330 and 335 are complementary todifferent portions of nucleic acid 305. These different portions ofnucleic acid 305 can be directly adjacent (e.g., without any interveningbases), or separated by one or more bases (e.g., separated by a knownSNP site, separated by a recognition site 150). Thus, when thecomplementary portions of nucleic acid 305 are separated by one or morebases, first and second genomic homology regions 330 and 335 will alsobe separated when the assay begins to convert MIP probe 310 intocircularized MIP probe 315, starting by hybridizing the first and secondgenomic homology regions 330 and 335 of MIP probe 310 to nucleic acid305. This separation, or gap, within MIP probe 315 is then filled byadding an appropriate base or bases and a polymerase to the assaysolution, which will add bases to the 3′ end of MIP probe 315. Thecircularization and conversion of MIP probe 310 into MIP probe 315 isthen completed through the use of an appropriate ligase. Thus, first andsecond genomic homology regions 330 and 335, which begin within MIPprobe 310 at opposite ends of the probe, become joined together to formcombined genomic homology region 380 of MIP probe 315. If first andsecond genomic homology regions 330 and 335 were separated by one ormore bases after hybridization to nucleic acid 305, then combinedgenomic homology region 380 will additionally include the bases whichwere added to fill the gap. After circularization of the MIP probes withtheir respective targets within the sample, the remaining nucleic acidsthat are present (e.g., non-circularized MIP probes and any remaininglinear nucleic acids from the sample), can be removed through anysuitable method, such as the use of an appropriate exonuclease (e.g.,Exo I).

Certain assay embodiments utilizing MIP probes do not employ anamplification step, and instead utilize the inherent high specificity ofMIP probes for their targets (due to the requirement that twohybridization events must occur between a particular probe and a regionof a nucleic acid within the sample at issue). Other assays, however, doutilize one or more amplification steps. This can occur utilizingcircularized MIP probe 315 through, for example, use of rolling circlereplication, or can occur through traditional PCR after linearization ofcircularized MIP probe 315 to produce linearized MIP probe 320. Withinassays that perform amplification after linearization of circularizedMIP probe 315, many embodiments utilize a MIP probe 310 thatadditionally comprises a first primer binding site 340 and a secondprimer binding site 345. First and second primer binding sites 340 and345 can function, for example, as forward and reverse PCR primer sitesfor linearized MIP probe 320. In certain embodiments, these PCR primersites are complementary to a set of universal primers such that aplurality of different MIP probes associated with a plurality of nucleicacids of interest each incorporate these universal primer sites, andtherefore facilitate amplification of all MIP probes (that arecircularized into MIP probes 315 and subsequently linearized into MIPprobes 320) with as few as a single set of PCR primers. Thus, increasingthe number of different MIP probes utilized within a particular assaycan facilitate a high level of multiplexing within the assay at issue.

MIP probe 310 may further comprise a cleavage site 350. Cleavage site350 facilitates the cleavage of circularized MIP probe 315 tore-linearize the probe and form MIP probe 320. Cleavage site 350 may bea restriction site for an appropriate enzyme, but may also employ othermechanisms to allow selective cleavage. For example, cleavage site 350may comprise one or more uracil bases to allow cleavage of circularizedMIP probe 315 through incubation with Uracil-DNA glycosylase to createone or more abasic sites for subsequent cleavage through an appropriatemeans (e.g., heat, an endonuclease that cleaves at abasic sites). Othermechanisms, such as the use of other modified bases and enzymes specificfor those modified bases, and which will create the abasic site andcleave the MIP probe, are also possible. Alternatively, a separateenzyme or mechanism (e.g., high temperature incubation) can be used tocleave the MIP probe at the created abasic sites. While the particularembodiment illustrated within FIG. 3 contains only one cleavage site350, other embodiments may use two or more cleavage sites 350 as may berequired or desirable for an assay. The particular embodimentillustrated within FIG. 3 positions cleavage site 350 between first andsecond primer binding sites 340 and 345. This positioning results in alinearized MIP probe 320 that place the first and second primer bindingsites 340 and 345 on opposite ends of the probe, thus facilitating theiruse as forward and reverse primer binding sites for PCR.

MIP probe 310 may additionally comprise a tag sequence 360. Tag sequence360 can comprise, for example, a unique sequence of nucleotides (uniquewithin the assay at issue) in order to provide a unique barcode for theMIP probe and any resulting amplicons which incorporate that particulartag sequence 360 from MIP probes that are circularized into MIP probes315 and then subsequently linearized into MIP probes 320. While the MIPprobe 310 illustrated within FIG. 3 only incorporates one tag sequence360, other embodiments may incorporate two or more tag sequences 360.For instance, a variation of MIP probe 310 can incorporate two differenttag sequences 360 in order to provide two unique sequences forsubsequent use within the assay to identify or correspond to variousaspects (e.g., the target sequence of nucleic acid 305, the samplewithin the assay to which MIP probe 310 was added). The one or more tagsequences 360 of linearized MIP probe 320 can be subsequently utilizedin a variety of means known in the art, including but not limited tohybridization with nucleic acid probes on a microarray (e.g., amicroarray with oligonucleotide probes complementary to tag sequence 360and/or its complement created within amplification), sequencing,real-time PCR, digital PCR, etc. Certain variations of tag sequences360, such as those which will be hybridized with a microarray, comprisea sequence that, when considered in the context of all of the tagsequences 360 at issue within an assay from the different MIP probes 310which are utilized, will maximize the mismatch between any pair of tagsequences 360 in order to minimize cross-hybridization.

MIP probe 310 may also comprise a restriction site 370. Restriction site370 can comprise, for example, a sequence recognized by a restrictionenzyme. Incorporation of restriction site 370 allows, within certainembodiments, the relevant sequence to be incorporated within theamplicons (assuming the embodiment utilizes amplification). Theamplicons can be maintained in double-stranded form if the restrictionsite 370 is for a restriction enzyme that recognizes and digests adouble-stranded recognition site, or the strands of the amplicons can beseparated for use with a restriction enzyme that digests asingle-stranded site. Even within assays that do not utilizeamplification, restriction site 370 can still be included within MIPprobe 310 and subsequently utilized. Restriction site 370 can be usedfor a variety of purposes in different assays, including but not limitedto separation of tag sequence 360 from combined genomic homology region380. For example, if a particular assay utilizes a tag microarray fordetection of tag sequences 360, restriction site 370 and itscorresponding restriction enzyme can be utilized to separate tagsequence 360 from combined genomic homology region 380 beforehybridization to the array. Preferably, the restriction site 370possesses a sequence that occurs infrequently to aid in avoiding itsoccurrence within the MIP probes within the assay at issue (e.g., toavoid having the sequence of restriction site 370 occur in the first orsecond genomic homology regions 330 and 335. As with tag sequence 360,certain embodiments may incorporate two or more restriction sites 370 asmay be necessary or desirable within particular assays. Otherembodiments of MIP probes may utilize only a portion of these describedfeatures, and in different quantities and/or for different functions.

FIGS. 4(A)-4(D) and 5(A)-5(C) illustrate a non-limiting embodimentutilizing certain embodiments of MIP probes, such as those describedabove and illustrated within FIG. 3, within a binding protein affinityassay. In these embodiments, MIP probes are used to selectively capture,and optionally amplify, target fragments 130 before hybridization tocapture oligonucleotides 120.

FIG. 4(A) illustrates a non-limiting embodiment of the initial, startingform of the MIP probe 410 that is added to the sample containing targetfragment 130. In the particular illustrated embodiment, MIP probe 410comprises first and second genomic homology regions 330 and 335, firstand second primer binding sites 340 and 345, cleavage site 350, tagsequence 360, and restriction site 370. As described above for FIG. 3,certain embodiments may omit one or more of these features. For example,if amplification of the circularized MIP probe is not going to beperformed, then first and second primer binding sites 340 and 345 areunnecessary. Alternatively, if tag sequence 360 will not be utilizedwithin the assay (e.g., a microarray with probes containingcomplementary sequences to the tags will not be used), then tag sequence360 can be omitted. In other variations in which tag sequence 360 isincluded and utilized, the tag sequence 360 is not separated fromcombined genomic homology region 380, and thus restriction site 370 maythus be unnecessary in such embodiments.

FIG. 4(B) illustrates a non-limiting example of MIP probe 410 afterhybridization with target fragment 130, thus creating partiallycircularized MIP probe 415. First and second genomic homology regions330 and 335 have hybridized to the portions of target fragment 130 forwhich they are respectively complementary. As depicted within FIG. 4(B),there is a gap between first and second genomic homology regions 330 and335. The size of the gap can vary depending on the embodiment and alsothe target fragment 130 (and its relevant recognition site 150) atissue. For example, if a purpose of the overall assay at issue is tocustomize the sequence of the recognition sites 150 to the particularindividual (e.g., a human patient being tested for their particularaffinities to different binding proteins as a precursor to thedetermination of a treatment path), then the gap desirably includes therecognition site 150 at issue. Accordingly, if the individual possessesone or more mutations affecting recognition site 150 (e.g., SNP(s)),then those mutations and their corresponding effects on binding proteinaffinities will be accounted for in the assay.

Other embodiments, however, may use a smaller gap that only includes aportion of the recognition site 150 at issue, which in certainembodiments may translate to a gap of a single nucleotide. Smaller gapsmay be utilized within embodiments that seek to test the affinity ofbinding proteins with respect to known SNPs within the recognition sites150. For instance, if a recognition site 150 is known to have aparticular SNP location, the corresponding first and second genomichomology regions 330 and 335 can be designed to leave a gapcorresponding to at least that location within target fragment 130.Thereafter, the resulting gap can be filled in the circularization ofMIP probe 415 by addition of the appropriate complementary base. Thus,the gap between first and second genomic homology regions 330 and 335may need to be different for each recognition site 150 at issue withinan assay, with the corresponding design of each MIP probe 410 reflectingthose differences. For instance, in contrast to the situation describedabove with a recognition site 150 being known to include a SNP location,the same assay may also involve a second recognition site 150 that isknown to include two SNP locations. The first and second genomichomology regions 330 and 335 for the MIP probe 410 utilized for thissecond recognition site would require a larger gap, in comparison to apossible gap of a single base with respect to a single SNP location, ifthe assay is to be customized to the particular genetic composition ofthe individual at issue.

FIG. 4(C) illustrates a non-limiting embodiment in which MIP probe 420has been circularized from MIP probe 415 by the addition of one or morebases 385 to fill the gap between first and second genomic homologyregions 330 and 335, thus creating combined genomic homology region 380after appropriate ligation.

FIG. 4(D) illustrates a non-limiting embodiment of linearized MIP probe425 after separation of MIP probe 420 from target fragment 130, andappropriate cleavage of MIP probe 420 at cleavage site 350. As anon-limiting example, cleavage site 350 can comprise three uracil bases,thus facilitating linearization of MIP probe 420 after treatment withuracil DNA glycosylase and endonuclease IV. The particular embodimentillustrated in FIG. 4(D) comprises first and second primer binding sites340 and 345, which after linearization of MIP probe 420 can be utilizedas forward and reverse PCR primer binding sites. If the sequencesutilized for first and second primer binding sites 340 and 345 areemployed for all MIP probes 410 included with a particular assay, then asingle set of universal primers may be employed for multiplexamplification of all MIP probes 425 at issue. Alternatively, the use ofmultiple sets of primers can be employed with two or more sets of firstand second primer binding sites 340 and 345 to facilitate selectiveamplification of MIP probes 425.

Additionally, the embodiment depicted in FIG. 4(D) contains arestriction site 370 between tag sequence 360 and combined genomichomology region 380. Use of an appropriate restriction enzyme forrestriction site 370 can be employed to separate tag sequence 360 andcombined genomic homology region 380 for subsequent use (e.g.,hybridization of combined genomic homology region 380 with captureoligonucleotide 120). Alternatively, if tag sequence 360 will not beutilized within a particular assay, the MIP probes 410 can omit tagsequence and/or restriction site 370 from their design.

FIGS. 5(A)-5(C) illustrate a non-limiting embodiment of subsequent useof linearized MIP probes 425 (and/or the complementary sequence that canbe amplified within the MIP assay) in a binding protein affinity assay.At this point within the assay, the MIP embodiment variants are similarin many respects to the non-limiting embodiments illustrated anddescribed within FIGS. 1(A)-1(C) and 2(A)-2(C). FIG. 5(A) depicts anon-limiting embodiment of MIP probe 425 hybridizing with a portion ofcapture oligonucleotide 120, which is attached to substrate 110. Theportion of MIP probe 425 to which capture oligonucleotide 120 hybridizeswill depend on the embodiment and the particular probes and captureoligonucleotides at issue. For example, in embodiments where a tagsequence 360 is utilized, all or a portion of capture oligonucleotide120 can be designed to be complementary to all or a portion of the tagsequence 360. Alternatively, other embodiments omit tag sequence 360 (orseparate tag sequence 360 from the rest of MIP probe 425 afterappropriate cutting at restriction site 370), and thus hybridize aportion or all of capture oligonucleotide 120 with a portion of, forinstance, combined genomic homology region 380.

As with earlier described embodiments, when the assay at issue is to becustomized to the individual at issue who provided the relevant sample,capture oligonucleotide 120 hybridizes to MIP probe 425 away fromrecognition site 150. This ensures that when complementary fragment 140is generated, such as within the non-limiting example illustrated withinFIG. 5(B), the completed double-stranded recognition site 150 and thesurrounding bases are exact to the individual, and contain any mutations(e.g., SNPs) that are possessed by the individual and which can affectthe binding affinity of one or more proteins. As before, complementaryfragment 140 may not be extended such that MIP probe 425 is completelydouble-stranded, but is extended to the point where recognition site 150is completely double-stranded (assuming the recognition site 150 isdesirably double-stranded, such as when the binding protein has apalindromic recognition site). However, also as before, if the bindingprotein at issue is specific for RNA or single-stranded DNA (or suchtargets are of interest in the assay and the double-stranded targetvariants are not), then as with the embodiments described in associationwith FIGS. 1(A)-1(C) and 2(A)-2(C), complementary fragment 140 will notbe generated.

FIG. 5(C) illustrates, as did FIGS. 1(C) and 2(C), a non-limitingexample of subsequent binding of a binding protein 160 to recognitionsite 150, and the use of a label 170 for use in determining the affinityof binding protein 160 for the particular recognition site 150. As withthe comparison of the embodiments for FIGS. 2(A)-2(C) relative to FIGS.1(A)-1(C), this step of the assay as depicted within FIG. 5(C) issubstantially similar in many respects.

The use of a MIP approach, according to the embodiments described inassociation with, for instance, the non-limiting examples within FIGS.2(A)-2(C) or 4(A)-4(D) and 5(A)-5(C), provides several additionaladvantages over embodiments such as those described in association withFIGS. 1(A)-1(C). For instance, the use of MIP technology allows captureof regions of interest with higher specificity than can often beobtained with the use of a single capture oligonucleotide 120 alone asdepicted in the non-limiting example within FIGS. 1(A)-1(C). It is wellknown that many binding proteins are specific are sequences that occurmultiple times throughout the genome, RNA transcripts, etc. of interest,and also that certain binding proteins possess at least a certain levelof general affinity for multiple different DNA or RNA sequences. Thus,depending on the assay configuration, it can be difficult to ensure thatthe assay is measuring the affinity of a binding protein for arecognition site 150 within a particular location of interest within thegenome, RNA transcripts, etc. that at issue within the assay.Embodiments which do not utilize a MIP approach within the overallassay, such as those embodiments illustrated within the non-limitingexample of FIGS. 1(A)-1(C), can compensate through a variety ofsolutions, such as, for example, use of unique sequences (and in someembodiments, sequences which are unique and conserved) within targetfragment 130 to hybridize with the capture oligonucleotides 120.

The use of MIP technology within an assay, however, such as withinembodiments illustrated within the non-limiting examples of FIGS.2(A)-2(C), 3, 4(A)-4(D) and 5(A)-5(C), can provide substantial benefits(in terms of ease of assay design and customization, implementation,accuracy, precision, and consistency) to ensure that the binding proteinaffinity portion of the assay is measuring the affinity of the bindingproteins for the recognition sites 150 of actual interest, and not thatof recognition sites possessing the same or a similar recognitionsequence that occur elsewhere in the genome, in RNA transcripts not ofinterest to the particular assay, etc. These benefits are largelyprovided by the inherent nature of the MIP probe structure in that twoseparate regions of the probe are required to cooperatively hybridizewith the target nucleic acid at issue, which results in a correspondingincrease in specificity in addition to an increased melting temperature(T_(m)) relative to a single region of hybridization, as well asproviding more rapid hybridization kinetics. Moreover, the ability torequire two separate regions for hybridization provides greaterflexibility (compared to the use of a single capture oligonucleotide120) in designing the probes for an assay that will capture therecognition site 150 within the target fragment 130 of interest, and notmerely a recognition site 150 that is present within some other sequencewithin the sample (with this other sequence possessing some level ofcomplementarity with capture oligonucleotide 120 such it hybridizes to acertain degree with capture oligonucleotide 120). As discussed earlier,the first and second genomic homology regions 330 and 335 can bedesigned to hybridize to the relevant target fragment 130 around therecognition site 150 of interest, thus allowing the gap fill portion ofthe reaction to add complementary bases and ensure that the resultingMIP probes (e.g., MIP probe 425) contain any mutations of the particularindividual that provided the sample (e.g., SNPs, insertions, deletions,indels) within the combined genomic homology region 380. In turn, thisensures that any effects of the mutations will affect the results of thebinding protein affinity portion of the assay.

Furthermore, other aspects of MIP technology facilitate the ease of usein the specific capture and downstream use of the precise recognitionsite 150 of interest. For instance, an in-solution use of MIP probes,such as the non-limiting example depicted within FIG. 4(A)-4(D), isutilized in many embodiments to selectively enrich the sample for thetarget fragments 130 containing the recognition sites 150 of interest.After addition of the MIP probes and their circularization, thenon-circularized MIP probes and single-stranded nucleic acids of thesample can be removed (e.g., with an exonuclease treatment that does notdegrade the circularized MIP probes). Combined with amplification of thecircularized MIP probes (e.g., after linearization and use of PCR primerbinding sites, or through rolling circle replication), the MIP approachthus greatly facilitates the introduction of nucleic acids to thearray(s) of capture oligonucleotides 120 a nucleic acid sample thatcontains an amplified amount of the desired target fragments 130 ofinterest while containing a non-existent or minimal amount of undesirednucleic acids.

MIP technology also facilitates other aspects of the binding proteinaffinity portion of the assay. For example, use of a unique tag sequence360 within MIP probe 410 (and which is present within MIP probe 425, orat least the complement of tag sequence 360) allows for hybridization ofMIP probe 410 at a specific location within a tag microarray whichpossesses capture oligonucleotides 120 with an appropriatelycomplementary sequence such that they hybridize with the tag sequence360 of MIP probes 425. Incorporation of a different tag sequence withineach MIP probe 410 allows that unique tag sequence 360 to accordinglydenote the particular location of the recognition site 150. Thus, whilea particular recognition sequence of a recognition site 150 may occurdozens, hundreds or thousands of times in a particular nucleic acidsample, the use of unique tag sequences 360 within a MIP approachfacilitates the binding affinity of the protein(s) at issue to beprecisely tested against the particular recognition site 150 ofinterest, and not merely other occurrences of the recognition sequence.This approach can thus be utilized to test a variety of recognitionsites 150, all of which may have the same recognition sequence and whichare binding targets for the same or similar binding proteins, within asingle assay while facilitating the differentiation of one recognitionsite 150 and its source location within the genome, RNA transcript, etc.from another recognition site 150 with the same recognition sequence bysimply having capture oligonucleotides 120 for different unique tagsequences 360 within different features of the microarray, attached todifferent distinguishable beads, or through other methods known in theart.

Many of the variations disclosed herein are desirably embodied within anassortment of kits. For example, kits are envisioned containing one ormore substrates 110 with attached capture oligonucleotides 120. Many kitembodiments will additionally contain the necessary reagents forpreparing a sample of nucleic acids for use with the captureoligonucleotides 120 (e.g., for amplification, purification,fragmentation, etc.). Furthermore, certain kit embodiments will alsocomprise binding proteins for use within the assay and/or the reagentsnecessary for in vitro translation of the binding proteins of interest(e.g., to create binding proteins of interest that are produced from themRNA of the individual that provided the sample to ensure that anyrelevant mutations from the individual are accounted for within thebinding protein affinity assay), and any associated molecules necessaryfor the assay (e.g., a cofactor necessary for the binding protein atissue to bind to its recognition site 150). Various kit embodiments willadditionally comprise one or more labels of one or more types for usewith the binding proteins and/or nucleic acids at issue within theassay, and may include, for example, various fluorescent labels,radioisotopes, and any necessary components for their use (e.g.,antibodies, biotin). Kits will often additionally comprise any otherreagents for the relevant assay. For instance, for embodiments whichutilize MIP technology (e.g., in creating MIP probes 425 for use in thebinding protein affinity assay as illustrated within the non-limitingexample of FIGS. 4(A)-4(D) and 5(A)-5(C)), the kits will additionallycomprise the MIP probes, enzymes, nucleotides, and other componentsnecessary to conduct the MIP portion of the assay as well.

It is to be understood that the above description is intended to beillustrative and not restrictive. Many variations of the invention willbe apparent to those of skill in the art upon reviewing the abovedescription. The scope of the invention should be determined withreference to the appended claims, along with the full scope ofequivalents to which such claims are entitled. All cited references,including patent and non-patent literature, are incorporated herewith byreference in their entireties for all purposes.

1. A method for measuring an affinity level of at least one binding protein for at least one recognition site, the method comprising: hybridizing a target fragment to a capture oligonucleotide; synthesizing a complementary fragment, wherein the complementary fragment extends the capture oligonucleotide and is complementary to the target fragment, and wherein synthesizing the complementary fragment creates a recognition site for a binding protein; introducing the binding protein to the recognition site; and measuring an affinity level of the binding protein for the recognition site.
 2. The method of claim 1, wherein the capture oligonucleotide is attached to a substrate. 3-4. (canceled)
 5. The method of claim 2, wherein multiple copies of the capture oligonucleotide is attached to the substrate.
 6. The method of claim 2, wherein a plurality of different capture oligonucleotides is attached to the substrate.
 7. The method of claim 2, wherein a plurality of different capture oligonucleotides is attached to the substrate, and wherein multiple copies of each different capture oligonucleotide are attached to the substrate.
 8. The method of claim 1, wherein the capture oligonucleotide comprises a complementary portion, and wherein the complementary portion is complementary to at least a portion of the target fragment.
 9. The method of claim 1, wherein hybridizing the target fragment to the capture oligonucleotide additionally comprises introducing a nucleic acid sample to the capture oligonucleotide, and wherein the nucleic acid sample comprises the target fragment.
 10. The method of claim 9, wherein the capture oligonucleotide comprises a complementary portion, and wherein the complementary portion is complementary to at least a portion of the target fragment. 11-17. (canceled)
 18. The method of claim 1, wherein the recognition site includes one or more mutations.
 19. The method of claim 18, wherein the one or more mutations is a single nucleotide polymorphism. 20-25. (canceled)
 26. The method of claim 1, wherein introducing the binding protein to the recognition site additionally comprises: introducing an antibody specific for the binding protein; and labeling the binding protein using the antibody.
 27. The method of claim 1, wherein introducing the binding protein to the recognition site additionally comprises: introducing one or more additional molecules selected from the group consisting of regulatory proteins, transcription cofactors and miRNAs, wherein the one or more additional molecules affect the affinity level of the binding protein for the recognition site. 28-30. (canceled)
 31. The method of claim 1, wherein hybridizing the target fragment to the capture oligonucleotide additionally comprises: hybridizing a second capture oligonucleotide to the target fragment, wherein the capture oligonucleotide and the second capture oligonucleotide cooperatively hybridize to the target fragment, and wherein the complementary fragment is synthesized such that the complementary fragment joins the capture oligonucleotide with the second capture oligonucleotide.
 32. The method of claim 1, additionally comprising: performing a selective capture and amplification of a nucleic acid sample to produce the target fragment hybridized to the capture oligonucleotide, wherein the selective capture and amplification comprise: hybridizing a target nucleic acid with a molecular inversion probe, wherein the molecular inversion probe comprises a first genomic homology region, a second genomic homology region, a first primer binding site, a second primer binding site and a cleavage site, wherein the first genomic homology region hybridizes to a first region of the target nucleic acid, wherein the second genomic homology region hybridizes to a second region of the target nucleic acid, and wherein the first and second genomic homology regions hybridize to the target nucleic acid such that a gap of one or more bases separate the first and second genomic homology regions; circularizing the molecular inversion probe, wherein circularization comprises creating a combined genomic homology region; linearizing the molecular inversion probe, wherein linearizing comprises cleaving the molecular inversion probe at the cleavage site; amplifying the combined genomic homology region by performing polymerase chain reaction to produce amplicons, wherein performing polymerase chain reaction includes using a first primer that is complementary to the first primer binding site and a second primer that is complementary to the second primer binding site, and wherein the amplicons are used as the target fragments hybridized to the capture oligonucleotides.
 33. The method of claim 32, wherein the gap includes the recognition site.
 34. The method of claim 32, wherein creating the combined genomic homology region comprises filling the gap with complementary nucleotides by extending one genomic homology region with a polymerase and ligating the first and second genomic homology regions after extension.
 35. The method of claim 32, wherein the molecular inversion probe additionally comprises a tag sequence, and wherein the tag sequence is amplified and incorporated within the amplicons.
 36. The method of claim 35, wherein at least a portion of the tag sequence is hybridized to the capture oligonucleotide.
 37. A method for measuring an affinity level of at least one binding protein for at least one recognition site, the method comprising: hybridizing a target fragment to a capture oligonucleotide, wherein the target fragment includes a recognition site for a binding protein; introducing the binding protein to the recognition site; and measuring an affinity level of the binding protein for the recognition site. 